6-31279637-C-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 0.393 in 151,900 control chromosomes in the GnomAD database, including 11,888 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 0.39 (11888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 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: 0.393 AC: 59684 AN: 151782 Hom.: 11873 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.393 AC: 59731 AN: 151900 Hom.: 11888 Cov.: 32 AF XY: 0.395 AC XY: 29293 AN XY: 74222

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.388

Alfa AF: 0.357 Hom.: 1199

Bravo AF: 0.392

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.71
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844608; hg19: chr6-31247414;