rs1711004

Variant names:

• chr3-188147631-A-G
• rs1711004
• ENST00000834038.1:n.583-505T>C

Variant summary

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

The ENST00000834038.1(ENSG00000308437):​n.583-505T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,906 control chromosomes in the GnomAD database, including 12,005 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 0.38 (12005 hom., cov: 31)
• Consequence: ENSG00000308437 ENST00000834038.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 2 publications found

Genes affected

ENSG00000308437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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
ENSG00000308437	ENST00000834038.1	n.583-505T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58014 AN: 151788 Hom.: 12009 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.382 AC: 58013 AN: 151906 Hom.: 12005 Cov.: 31 AF XY: 0.377 AC XY: 27969 AN XY: 74250

African (AFR) AF: 0.220 AC: 9100 AN: 41422

American (AMR) AF: 0.365 AC: 5569 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2538 AN: 5144

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4351 AN: 10550

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32300 AN: 67944

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.419 Hom.: 6023

Bravo AF: 0.374

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.42
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1711004; hg19: chr3-187865419; COSMIC: COSV71384682;