11-641191-C-A

Position:

• chr11-641191-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.48 in 152,170 control chromosomes in the GnomAD database, including 17,968 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 0.48 (17968 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.480 AC: 73011 AN: 152052 Hom.: 17958 Cov.: 35

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.480 AC: 73065 AN: 152170 Hom.: 17968 Cov.: 35 AF XY: 0.483 AC XY: 35956 AN XY: 74396

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.476

Alfa AF: 0.502 Hom.: 21345

Bravo AF: 0.479

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11246226; hg19: chr11-641191;