rs1940163

Variant names:

• chr11-95973878-C-A
• rs1940163

Your query was ambiguous. Multiple possible variants found:

• chr11-95973878-C-A
• chr11-95973878-C-T

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 0.439 in 152,008 control chromosomes in the GnomAD database, including 16,257 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 0.44 (16257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.439 AC: 66647 AN: 151892 Hom.: 16223 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.439 AC: 66732 AN: 152008 Hom.: 16257 Cov.: 32 AF XY: 0.446 AC XY: 33127 AN XY: 74290

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.406

Alfa AF: 0.336 Hom.: 17710

Bravo AF: 0.446

Asia WGS AF: 0.470 AC: 1632 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.70
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1940163; hg19: chr11-95707042;