rs7679673

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The ENST00000504082.1(ENSG00000251259):n.110+133G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000504082.1 is not a MANE Select or MANE Plus Clinical transcript for ENSG00000251259; 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 0.507 (AC=77,071) in the gnomAD database across 152,018 control chromosomes, including 20,408 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.781. 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 0.51 ( 20408 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

ENSG00000251259
ENST00000504082.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350

Publications

141 publications found

Variant links:

Genes affected

LOC124900868 (HGNC:):

LOC124900868 links:

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new If you want to explore the variant's impact on the transcript ENST00000504082.1, 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 ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -4 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.781 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000504082.1. 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	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
ENSG00000251259 ENST00000504082.1	TSL:4	n.110+133G>T	intron	Intron 1 of 1	Prot:
ENSG00000251259 ENST00000776606.1		n.149-2659G>T	intron	Intron 1 of 1	Prot:
ENSG00000251259 ENST00000776607.1		n.371-2659G>T	intron	Intron 2 of 2	Prot:

ENSG00000251259 ENST00000504082.1

TSL:4

HGVSc / HGVSpn.110+133G>T

Exon rankIntron 1 of 1

intron

Prot:

ENSG00000251259 ENST00000776606.1

HGVSc / HGVSpn.149-2659G>T

Exon rankIntron 1 of 1

intron

Prot:

ENSG00000251259 ENST00000776607.1

HGVSc / HGVSpn.371-2659G>T

Exon rankIntron 2 of 2

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 5 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.507	AC:76970	Hom:20369	AN:151900	Cov:32
GnomAD4 exome Warning	AF:	AC:0	Hom:0	AN:0	Cov:
GnomAD4 genome	AF: 0.507	AC:77071	Hom:20408	AN:152018	Cov:32
TOPMed (Bravo)	AF: 0.510	AC:135119	Hom:36030	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.441	AC:237000	Hom:54414	AN:537562	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.483	AC:1132	Hom:297	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.803	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.340	AC:102	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.681	AC:2361	Hom:	AN:3476	Cov:
Korea4K (4,157 Koreans)	AF: 0.811	AC:5863	Hom:	AN:7226	Cov:
Qatari Genome	AF: 0.551	AC:97	Hom:	AN:176	Cov:
Turkish Variome	AF: 0.523	AC:809	Hom:212	AN:1546	Cov:
UK10K	AF: 0.375	AC:2835	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.807	AC:7230	Hom:2924	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	2.1
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.30
GPN-Star LLR	N/A	5.8
GPN-Star score	N/A	1.3
PhyloP100	Benign	0.035

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 ACGS-UK Somatic Oncogenicity v2025

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