6-31479019-G-A

Position:

• chr6-31479019-G-A

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 0.194 in 151,792 control chromosomes in the GnomAD database, including 3,184 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 0.19 (3184 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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 (AMR) allele frequency at 95% confidence interval = 0.254 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: 0.194 AC: 29427 AN: 151670 Hom.: 3179 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.194 AC: 29452 AN: 151792 Hom.: 3184 Cov.: 32 AF XY: 0.194 AC XY: 14419 AN XY: 74212

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.200

Alfa AF: 0.215 Hom.: 5528

Bravo AF: 0.201

Asia WGS AF: 0.172 AC: 600 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248462; hg19: chr6-31446796;