rs7267944

Positions:

• chr20-39318791-T-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 0.252 in 152,162 control chromosomes in the GnomAD database, including 5,724 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 0.25 (5724 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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: 0.252 AC: 38279 AN: 152044 Hom.: 5706 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.252 AC: 38336 AN: 152162 Hom.: 5724 Cov.: 33 AF XY: 0.250 AC XY: 18598 AN XY: 74410

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.237

Alfa AF: 0.196 Hom.: 2520

Bravo AF: 0.259

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7267944; hg19: chr20-37947434;