rs7263053

Variant names:

• chr20-48434784-C-T
• rs7263053

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.268 in 152,108 control chromosomes in the GnomAD database, including 5,747 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 0.27 (5747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.268 AC: 40711 AN: 151990 Hom.: 5725 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.268 AC: 40770 AN: 152108 Hom.: 5747 Cov.: 32 AF XY: 0.264 AC XY: 19645 AN XY: 74354

African (AFR) AF: 0.322 AC: 13341 AN: 41464

American (AMR) AF: 0.224 AC: 3419 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5166

South Asian (SAS) AF: 0.297 AC: 1430 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10604

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17634 AN: 67986

Other (OTH) AF: 0.259 AC: 545 AN: 2106

Alfa AF: 0.264 Hom.: 2901

Bravo AF: 0.276

Asia WGS AF: 0.282 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7263053; hg19: chr20-47063526;