rs1377896

Variant names:

• chr4-32372317-C-A
• rs1377896

Your query was ambiguous. Multiple possible variants found:

• chr4-32372317-C-A
• chr4-32372317-C-G
• chr4-32372317-C-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 0.231 in 151,552 control chromosomes in the GnomAD database, including 5,132 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 0.23 (5132 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63
• 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 = 0.493 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34894 AN: 151436 Hom.: 5123 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.231 AC: 34942 AN: 151552 Hom.: 5132 Cov.: 31 AF XY: 0.232 AC XY: 17207 AN XY: 74082

African (AFR) AF: 0.355 AC: 14691 AN: 41352

American (AMR) AF: 0.348 AC: 5297 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3460

East Asian (EAS) AF: 0.509 AC: 2611 AN: 5132

South Asian (SAS) AF: 0.187 AC: 902 AN: 4818

European-Finnish (FIN) AF: 0.0778 AC: 824 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9454 AN: 67688

Other (OTH) AF: 0.236 AC: 498 AN: 2106

Alfa AF: 0.170 Hom.: 11655

Bravo AF: 0.260

Asia WGS AF: 0.355 AC: 1232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.35
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs1377896; hg19: chr4-32373939;