6-31284619-A-C

Position:

• chr6-31284619-A-C

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 0.813 in 152,146 control chromosomes in the GnomAD database, including 50,886 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 0.81 (50886 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.813 AC: 123637 AN: 152028 Hom.: 50830 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.813 AC: 123746 AN: 152146 Hom.: 50886 Cov.: 31 AF XY: 0.819 AC XY: 60876 AN XY: 74364

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.857

Alfa AF: 0.760 Hom.: 49078

Bravo AF: 0.823

Asia WGS AF: 0.882 AC: 3067 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524054; hg19: chr6-31252396;