rs2350811

chr6-115556347-T-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 0.74 in 152,076 control chromosomes in the GnomAD database, including 42,616 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 0.74 (42616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 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: 0.740 AC: 112467 AN: 151958 Hom.: 42562 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.740 AC: 112586 AN: 152076 Hom.: 42616 Cov.: 32 AF XY: 0.732 AC XY: 54445 AN XY: 74336

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.709

Alfa AF: 0.724 Hom.: 6809

Bravo AF: 0.755

Asia WGS AF: 0.708 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2350811; hg19: chr6-115877511;