rs1911877

Variant names:

• chr4-131377084-T-C
• rs1911877

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.341 in 152,036 control chromosomes in the GnomAD database, including 9,006 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 0.34 (9006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.341 AC: 51833 AN: 151918 Hom.: 8993 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.341 AC: 51893 AN: 152036 Hom.: 9006 Cov.: 32 AF XY: 0.338 AC XY: 25119 AN XY: 74316

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.363

Alfa AF: 0.339 Hom.: 10708

Bravo AF: 0.351

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1911877; hg19: chr4-132298239;