rs1564632

Variant names:

• chr11-7895165-C-A
• rs1564632
• ENST00000527847.5:n.353+10438G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-7895165-C-A
• chr11-7895165-C-T

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

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

The NR_036678.1(LOC283299):n.353+10438G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_036678.1 is not a MANE Select or MANE Plus Clinical transcript for LOC283299; 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 0.233 (AC=35,361) in the gnomAD database across 152,042 control chromosomes, including 4,382 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.29. 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 0.23 (4382 hom., cov: 32)
• Consequence: LOC283299 NR_036678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 2 publications found

Genes affected

ENSG00000254951 (HGNC:):

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

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

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 = 0.2895 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_036678.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	LOC283299 NR_036678.1		n.353+10438G>T	intron	Intron 1 of 7	Prot:

LOC283299 NR_036678.1

HGVSc / HGVSpn.353+10438G>T

Exon rankIntron 1 of 7

intron

Prot:

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ENSG00000254951 ENST00000527847.5	TSL:2	n.353+10438G>T	intron	Intron 1 of 7	Prot:
	ENSG00000254951 ENST00000718815.1		n.373+10438G>T	intron	Intron 2 of 2	Prot:

ENSG00000254951 ENST00000527847.5

TSL:2

HGVSc / HGVSpn.353+10438G>T

Exon rankIntron 1 of 7

intron

Prot:

ENSG00000254951 ENST00000718815.1

HGVSc / HGVSpn.373+10438G>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 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.232	AC:35311	Hom:4371	AN:151926	Cov:32
GnomAD4 genome	AF: 0.233	AC:35361	Hom:4382	AN:152042	Cov:32
TOPMed (Bravo)	AF: 0.237	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.199	AC:22744	Hom:2536	AN:114042	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.243	AC:570	Hom:64	AN:2342	Cov:
Denmark Genome	AF: 0.150	AC:45	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.164	AC:572	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.155	AC:1123	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.233	AC:41	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.187	AC:22912	Hom:2127	AN:122656	Cov:
Turkish Variome	AF: 0.224	AC:347	Hom:45	AN:1546	Cov:
UK10K	AF: 0.201	AC:1519	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.125	AC:1119	Hom:75	AN:8960	Cov:

Showing 13 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	9.9
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.76
GPN-Star LLR	N/A	0.31
GPN-Star score	N/A	-0.31
PhyloP100	Benign	-0.41

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.

Other links and lift over

dbSNP: rs1564632;

hg19: chr11-7916712;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar