6-115663255-T-G

Variant names:

• chr6-115663255-T-G
• rs4946111

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 0.506 in 151,944 control chromosomes in the GnomAD database, including 19,742 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 0.51 (19742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 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: 0.507 AC: 76905 AN: 151828 Hom.: 19732 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.506 AC: 76951 AN: 151944 Hom.: 19742 Cov.: 32 AF XY: 0.503 AC XY: 37378 AN XY: 74276

African (AFR) AF: 0.434 AC: 17998 AN: 41454

American (AMR) AF: 0.550 AC: 8369 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5166

South Asian (SAS) AF: 0.522 AC: 2515 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5620 AN: 10564

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36825 AN: 67930

Other (OTH) AF: 0.503 AC: 1061 AN: 2108

Alfa AF: 0.394 Hom.: 1056

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.29
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs4946111; hg19: chr6-115984419;