chr6-31842308-G-T

Position:

• chr6-31842308-G-T

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 0.224 in 152,022 control chromosomes in the GnomAD database, including 4,409 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 0.22 (4409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.224 AC: 34014 AN: 151904 Hom.: 4405 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.224 AC: 34053 AN: 152022 Hom.: 4409 Cov.: 32 AF XY: 0.232 AC XY: 17255 AN XY: 74328

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.204

Alfa AF: 0.154 Hom.: 3170

Bravo AF: 0.222

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3115673; hg19: chr6-31810085;