rs7272481

chr20-19181915-A-Gchr20-19181915-A-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 0.125 in 152,178 control chromosomes in the GnomAD database, including 1,268 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 0.13 (1268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.125 AC: 19059 AN: 152062 Hom.: 1261 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0740

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.125 AC: 19095 AN: 152178 Hom.: 1268 Cov.: 32 AF XY: 0.125 AC XY: 9298 AN XY: 74410

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.0740

Gnomad4 EAS AF: 0.0339

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.101

Alfa AF: 0.127 Hom.: 2802

Bravo AF: 0.121

Asia WGS AF: 0.0640 AC: 222 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	1.9
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7272481; hg19: chr20-19162559;