11-102845590-A-G

Variant names:

• chr11-102845590-A-G
• rs645419

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 0.57 in 152,004 control chromosomes in the GnomAD database, including 25,216 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 0.57 (25216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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: 0.570 AC: 86590 AN: 151886 Hom.: 25178 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.570 AC: 86683 AN: 152004 Hom.: 25216 Cov.: 32 AF XY: 0.579 AC XY: 43022 AN XY: 74280

African (AFR) AF: 0.635 AC: 26348 AN: 41482

American (AMR) AF: 0.635 AC: 9705 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3469 AN: 5152

South Asian (SAS) AF: 0.699 AC: 3371 AN: 4824

European-Finnish (FIN) AF: 0.607 AC: 6397 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33390 AN: 67938

Other (OTH) AF: 0.556 AC: 1173 AN: 2110

Alfa AF: 0.522 Hom.: 30161

Bravo AF: 0.575

Asia WGS AF: 0.666 AC: 2316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.33
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs645419; hg19: chr11-102716321;