11-91080629-G-C

Position:

• chr11-91080629-G-C

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 0.139 in 152,058 control chromosomes in the GnomAD database, including 1,513 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 0.14 (1513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21163 AN: 151940 Hom.: 1512 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21159 AN: 152058 Hom.: 1513 Cov.: 32 AF XY: 0.139 AC XY: 10320 AN XY: 74324

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0454 Hom.: 27

Bravo AF: 0.144

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.034
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534600; hg19: chr11-90813797;