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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.648 AC: 26874 AN: 41460

American (AMR) AF: 0.437 AC: 6679 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2473 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2332 AN: 4814

European-Finnish (FIN) AF: 0.417 AC: 4396 AN: 10534

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21862 AN: 67978

Other (OTH) AF: 0.406 AC: 857 AN: 2112

Alfa AF: 0.351 Hom.: 42206

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1940163; hg19: chr11-95707042;