rs2705511

Variant names:

• chr3-112460632-A-C
• rs2705511
• ENST00000793585.1:n.392+39723A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-112460632-A-C
• chr3-112460632-A-G
• chr3-112460632-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000793585.1(ENSG00000303317):​n.392+39723A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,036 control chromosomes in the GnomAD database, including 8,443 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8443 hom., cov: 32)
• Consequence: ENSG00000303317 ENST00000793585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 10 publications found

Genes affected

ENSG00000303317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303317	ENST00000793585.1	n.392+39723A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47864 AN: 151918 Hom.: 8411 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.288

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.315 AC: 47946 AN: 152036 Hom.: 8443 Cov.: 32 AF XY: 0.325 AC XY: 24128 AN XY: 74312

African (AFR) AF: 0.352 AC: 14597 AN: 41464

American (AMR) AF: 0.380 AC: 5802 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3763 AN: 5160

South Asian (SAS) AF: 0.517 AC: 2491 AN: 4816

European-Finnish (FIN) AF: 0.314 AC: 3321 AN: 10564

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16140 AN: 67966

Other (OTH) AF: 0.294 AC: 620 AN: 2110

Alfa AF: 0.160 Hom.: 327

Bravo AF: 0.322

Asia WGS AF: 0.595 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2705511; hg19: chr3-112179479;