rs7267944

Variant names:

• chr20-39318791-T-C
• rs7267944

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;