rs717376

Variant names:

• chr4-12077975-G-A
• rs717376

Your query was ambiguous. Multiple possible variants found:

• chr4-12077975-G-A
• chr4-12077975-G-C
• chr4-12077975-G-T

Variant summary

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

The variant allele was found at a frequency of 0.322 in 151,964 control chromosomes in the GnomAD database, including 9,588 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 (9588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48860 AN: 151846 Hom.: 9592 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.322 AC: 48873 AN: 151964 Hom.: 9588 Cov.: 32 AF XY: 0.328 AC XY: 24397 AN XY: 74268

African (AFR) AF: 0.100 AC: 4157 AN: 41488

American (AMR) AF: 0.378 AC: 5758 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1184 AN: 3464

East Asian (EAS) AF: 0.615 AC: 3165 AN: 5150

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4816

European-Finnish (FIN) AF: 0.508 AC: 5367 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26564 AN: 67930

Other (OTH) AF: 0.338 AC: 712 AN: 2106

Alfa AF: 0.351 Hom.: 5269

Bravo AF: 0.302

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs717376; hg19: chr4-12079599;