11-643568-G-C

Variant names:

• chr11-643568-G-C
• rs936465

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 0.509 in 152,070 control chromosomes in the GnomAD database, including 19,967 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 0.51 (19967 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.722 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: 0.509 AC: 77315 AN: 151952 Hom.: 19943 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.509 AC: 77390 AN: 152070 Hom.: 19967 Cov.: 33 AF XY: 0.512 AC XY: 38068 AN XY: 74320

African (AFR) AF: 0.449 AC: 18623 AN: 41476

American (AMR) AF: 0.543 AC: 8302 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3818 AN: 5150

South Asian (SAS) AF: 0.596 AC: 2876 AN: 4824

European-Finnish (FIN) AF: 0.483 AC: 5115 AN: 10590

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35190 AN: 67964

Other (OTH) AF: 0.509 AC: 1072 AN: 2108

Alfa AF: 0.503 Hom.: 2416

Bravo AF: 0.510

Asia WGS AF: 0.628 AC: 2186 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	1.5
DANN	Benign	0.42
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs936465; hg19: chr11-643568;