6-31218249-A-T

Variant names:

• chr6-31218249-A-T
• rs9263963

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 0.122 in 152,212 control chromosomes in the GnomAD database, including 1,249 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 0.12 (1249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.156 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: 0.122 AC: 18559 AN: 152094 Hom.: 1247 Cov.: 32

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.122 AC: 18579 AN: 152212 Hom.: 1249 Cov.: 32 AF XY: 0.126 AC XY: 9404 AN XY: 74416

African (AFR) AF: 0.0983 AC: 4084 AN: 41530

American (AMR) AF: 0.162 AC: 2469 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3468

East Asian (EAS) AF: 0.109 AC: 568 AN: 5192

South Asian (SAS) AF: 0.139 AC: 669 AN: 4818

European-Finnish (FIN) AF: 0.185 AC: 1955 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7625 AN: 68010

Other (OTH) AF: 0.170 AC: 360 AN: 2116

Alfa AF: 0.0507 Hom.: 52

Bravo AF: 0.122

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.7
DANN	Benign	0.94
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9263963; hg19: chr6-31186026;