rs726640

Variant names:

• chr1-159685728-G-A
• rs726640
• ENST00000751816.1:n.107+25039G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159685728-G-A
• chr1-159685728-G-C
• chr1-159685728-G-T

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 ENST00000751816.1(ENSG00000297913):n.107+25039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000751816.1 is not a MANE Select or MANE Plus Clinical transcript for ENSG00000297913; 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 0.0479 (AC=7,298) in the gnomAD database across 152,210 control chromosomes, including 587 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.164. 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 0.048 (587 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 6 publications found

Genes affected

ENSG00000297913 (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 = 0.164 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913 ENST00000751816.1		n.107+25039G>A	intron	Intron 1 of 2	Prot:
	ENSG00000297913 ENST00000751817.1		n.109+25039G>A	intron	Intron 1 of 3	Prot:
	ENSG00000297913 ENST00000751818.1		n.62+25039G>A	intron	Intron 1 of 2	Prot:

ENSG00000297913 ENST00000751816.1

HGVSc / HGVSpn.107+25039G>A

Exon rankIntron 1 of 2

intron

Prot:

ENSG00000297913 ENST00000751817.1

HGVSc / HGVSpn.109+25039G>A

Exon rankIntron 1 of 3

intron

Prot:

ENSG00000297913 ENST00000751818.1

HGVSc / HGVSpn.62+25039G>A

Exon rankIntron 1 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: 0.0480	AC:7295	Hom:588	AN:152092	Cov:31
GnomAD4 genome	AF: 0.0479	AC:7298	Hom:587	AN:152210	Cov:31
TOPMed (Bravo)	AF: 0.0554	AC:14661	Hom:1212	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0161	AC:10697	Hom:825	AN:664574	Cov:
Local & regional cohorts 6 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.0397	AC:93	Hom:3	AN:2342	Cov:
GenomeAsia100K	AF: 0.00895	AC:32	Hom:	AN:3478	Cov:
Qatari Genome	AF: 0.0114	AC:2	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.00000800	AC:1	Hom:0	AN:122660	Cov:
Turkish Variome	AF: 0.000647	AC:1	Hom:0	AN:1546	Cov:
UK10K	AF: 0.000397	AC:3	Hom:	AN:7562	Cov:

Showing 10 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	6.5
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.6
DANN	Benign	0.79
GPN-Star LLR	N/A	0.23
GPN-Star score	N/A	-0.23
PhyloP100	Benign	0.49

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: rs726640;

hg19: chr1-159655518;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar