chr11-20556298-T-A

Variant names:

• chr11-20556298-T-A
• rs10741845

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 0.401 in 152,058 control chromosomes in the GnomAD database, including 13,914 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 0.40 (13914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60938 AN: 151940 Hom.: 13908 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.401 AC: 60942 AN: 152058 Hom.: 13914 Cov.: 32 AF XY: 0.407 AC XY: 30219 AN XY: 74304

African (AFR) AF: 0.175 AC: 7252 AN: 41498

American (AMR) AF: 0.405 AC: 6186 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1714 AN: 3464

East Asian (EAS) AF: 0.270 AC: 1392 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2143 AN: 4814

European-Finnish (FIN) AF: 0.606 AC: 6409 AN: 10570

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34496 AN: 67964

Other (OTH) AF: 0.422 AC: 889 AN: 2106

Alfa AF: 0.441 Hom.: 1939

Bravo AF: 0.368

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.15
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10741845; hg19: chr11-20577844;