11-9573341-G-C

Variant names:

• chr11-9573341-G-C
• rs3763868

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 0.582 in 152,118 control chromosomes in the GnomAD database, including 26,191 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 0.58 (26191 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88470 AN: 151998 Hom.: 26164 Cov.: 34

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.582 AC: 88550 AN: 152118 Hom.: 26191 Cov.: 34 AF XY: 0.583 AC XY: 43357 AN XY: 74366

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.534

Alfa AF: 0.509 Hom.: 1583

Bravo AF: 0.562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.6
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763868; hg19: chr11-9594888;