6-115556347-T-C

Variant names:

• chr6-115556347-T-C
• rs2350811

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 0.74 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.902 AC: 37457 AN: 41516

American (AMR) AF: 0.691 AC: 10543 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2066 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2919 AN: 5170

South Asian (SAS) AF: 0.738 AC: 3551 AN: 4812

European-Finnish (FIN) AF: 0.602 AC: 6368 AN: 10580

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47301 AN: 67958

Other (OTH) AF: 0.709 AC: 1491 AN: 2104

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2350811; hg19: chr6-115877511;