chr18-49655298-A-T

Variant names:

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The XR_007066363.1(LOC105372112):n.179-6736A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: XR_007066363.1 is not a MANE Select or MANE Plus Clinical transcript for LOC105372112; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.878 (AC=133,653) in the gnomAD database across 152,206 control chromosomes, including 58,950 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.953. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.88 ( 58950 hom., cov: 31)

Consequence

LOC105372112
XR_007066363.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

79 publications found

Variant links:

Genes affected

ENSG00000310339 (HGNC:):

ENSG00000310339 links:

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new If you want to explore the variant's impact on the transcript XR_007066363.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Benign. The variant received -12 points.

Show applied only (2)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.9528 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000849189.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Gene / Transcript	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
ENSG00000310339 ENST00000849189.1	n.248+4539A>T	intron	Intron 1 of 3	Prot:
ENSG00000310339 ENST00000849192.1	n.232-1589A>T	intron	Intron 1 of 1	Prot:
ENSG00000310339 ENST00000849193.1	n.276-1589A>T	intron	Intron 1 of 1	Prot:

ENSG00000310339 ENST00000849189.1

HGVSc / HGVSpn.248+4539A>T

Exon rankIntron 1 of 3

intron

Prot:

ENSG00000310339 ENST00000849192.1

HGVSc / HGVSpn.232-1589A>T

Exon rankIntron 1 of 1

intron

Prot:

ENSG00000310339 ENST00000849193.1

HGVSc / HGVSpn.276-1589A>T

Exon rankIntron 1 of 1

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.878	AC:133531	Hom:58890	AN:152088	Cov:31
GnomAD4 genome	AF: 0.878	AC:133653	Hom:58950	AN:152206	Cov:31
TOPMed (Bravo)	AF: 0.888	AC:235172	Hom:104966	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.866	AC:20321	Hom:8852	AN:23468	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.907	AC:2124	Hom:963	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.819	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.813	AC:244	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.870	AC:3026	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.841	AC:6084	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.852	AC:150	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.855	AC:105001	Hom:44966	AN:122785	Cov:
Turkish Variome	AF: 0.906	AC:1400	Hom:633	AN:1546	Cov:
UK10K	AF: 0.825	AC:6238	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.824	AC:7379	Hom:3041	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	1.7
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.72
GPN-Star LLR	N/A	4.2
GPN-Star score	N/A	-0.69
PhyloP100	Benign	0.015

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence