rs3093077

Variant names:

• chr1-159709846-A-C
• rs3093077
• ENST00000751816.1:n.108-16681A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-159709846-A-C
• chr1-159709846-A-G
• chr1-159709846-A-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 ENST00000751816.1(ENSG00000297913):n.108-16681A>C 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 0.136 (AC=20,686) in the gnomAD database across 152,230 control chromosomes, including 2,276 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.297. 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 0.14 (2276 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 89 publications found

Genes affected

ENSG00000297913 (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 = 0.2968 — exceeds 5%% threshold (BA1 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
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.108-16681A>C		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-16681A>C		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-16681A>C		intron	N/A

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: 0.136	AC:20644	Hom:2265	AN:152112	Cov:32
GnomAD4 genome	AF: 0.136	AC:20686	Hom:2276	AN:152230	Cov:32
TOPMed (Bravo)	AF: 0.143	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0857	AC:45039	Hom:3343	AN:525352	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.122	AC:285	Hom:26	AN:2340	Cov:
ChinaMAP Phase 1	AF: 0.174	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.0567	AC:17	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.113	AC:391	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.146	AC:1057	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.278	AC:49	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.134	AC:16459	Hom:1143	AN:122726	Cov:
Turkish Variome	AF: 0.118	AC:183	Hom:9	AN:1546	Cov:
UK10K	AF: 0.0594	AC:449	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.180	AC:1615	Hom:148	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	1.8
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.66
GPN-Star LLR	N/A	0.29
GPN-Star score	N/A	-0.29
PhyloP100	Benign	-0.79

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.

Other links and lift over

dbSNP: rs3093077;

hg19: chr1-159679636;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar