rs6457620

Positions:

• chr6-32696222-G-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 0.519 in 151,732 control chromosomes in the GnomAD database, including 20,817 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 0.52 (20817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78641 AN: 151612 Hom.: 20792 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.519 AC: 78724 AN: 151732 Hom.: 20817 Cov.: 31 AF XY: 0.522 AC XY: 38654 AN XY: 74108

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.543

Alfa AF: 0.517 Hom.: 2559

Bravo AF: 0.528

Asia WGS AF: 0.533 AC: 1858 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	4.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6457620; hg19: chr6-32663999;