rs967417

chr20-6640246-G-Achr20-6640246-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 0.416 in 151,822 control chromosomes in the GnomAD database, including 14,783 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 0.42 (14783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.416 AC: 63101 AN: 151702 Hom.: 14764 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.416 AC: 63147 AN: 151822 Hom.: 14783 Cov.: 31 AF XY: 0.426 AC XY: 31618 AN XY: 74196

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.419

Alfa AF: 0.459 Hom.: 38412

Bravo AF: 0.407

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.28
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs967417; hg19: chr20-6620893;