rs486975

Variant names:

• chr11-94336325-T-A
• rs486975

Your query was ambiguous. Multiple possible variants found:

• chr11-94336325-T-A
• chr11-94336325-T-C
• chr11-94336325-T-G

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 0.527 in 151,814 control chromosomes in the GnomAD database, including 22,191 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 0.53 (22191 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79891 AN: 151694 Hom.: 22181 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.527 AC: 79931 AN: 151814 Hom.: 22191 Cov.: 31 AF XY: 0.529 AC XY: 39242 AN XY: 74168

African (AFR) AF: 0.337 AC: 13954 AN: 41386

American (AMR) AF: 0.563 AC: 8597 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2269 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3203 AN: 5128

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4816

European-Finnish (FIN) AF: 0.648 AC: 6802 AN: 10500

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40769 AN: 67938

Other (OTH) AF: 0.558 AC: 1180 AN: 2114

Alfa AF: 0.558 Hom.: 3084

Bravo AF: 0.515

Asia WGS AF: 0.546 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.87
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs486975; hg19: chr11-94069491; COSMIC: COSV69616528;