chr14-60606157-T-C

Variant names:

• chr14-60606157-T-C
• rs10483727
• ENST00000827601.1:n.467+4876A>G

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

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

The ENST00000827601.1(ENSG00000307639):n.467+4876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000827601.1 is not a MANE Select or MANE Plus Clinical transcript for ENSG00000307639; 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 0.456 (AC=69,380) in the gnomAD database across 152,230 control chromosomes, including 19,819 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.6. 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 0.46 (19819 hom., cov: 32)
• Consequence: ENSG00000307639 ENST00000827601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 107 publications found

Genes affected

ENSG00000307639 (HGNC:):

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

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

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 = 0.6 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000827601.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ENSG00000307639 ENST00000827601.1		n.467+4876A>G	intron	Intron 3 of 3	Prot:
	ENSG00000307639 ENST00000827602.1		n.405-30865A>G	intron	Intron 2 of 2	Prot:
	ENSG00000307639 ENST00000827603.1		n.497+4840A>G	intron	Intron 3 of 3	Prot:

ENSG00000307639 ENST00000827601.1

HGVSc / HGVSpn.467+4876A>G

Exon rankIntron 3 of 3

intron

Prot:

ENSG00000307639 ENST00000827602.1

HGVSc / HGVSpn.405-30865A>G

Exon rankIntron 2 of 2

intron

Prot:

ENSG00000307639 ENST00000827603.1

HGVSc / HGVSpn.497+4840A>G

Exon rankIntron 3 of 3

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: 0.456	AC:69357	Hom:19813	AN:152112	Cov:32
GnomAD4 genome	AF: 0.456	AC:69380	Hom:19819	AN:152230	Cov:32
TOPMed (Bravo)	AF: 0.432	AC:114247	Hom:31120	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.539	AC:382994	Hom:111181	AN:710836	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.455	AC:1066	Hom:253	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.249	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.597	AC:179	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.333	AC:1159	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.276	AC:1999	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.290	AC:51	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.224	AC:27555	Hom:3146	AN:122802	Cov:
Turkish Variome	AF: 0.486	AC:751	Hom:178	AN:1546	Cov:
UK10K	AF: 0.596	AC:4508	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.226	AC:2021	Hom:236	AN:8960	Cov:

Showing 14 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	8.6
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.65
GPN-Star LLR	N/A	-1.8
GPN-Star score	N/A	1.8
PhyloP100	Benign	0.64

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: rs10483727;

hg19: chr14-61072875;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar