rs7252567

Variant names:

• chr19-45375347-C-T
• rs7252567

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 0.303 in 151,214 control chromosomes in the GnomAD database, including 9,973 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 0.30 (9973 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.302 AC: 45684 AN: 151098 Hom.: 9946 Cov.: 29

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.303 AC: 45761 AN: 151214 Hom.: 9973 Cov.: 29 AF XY: 0.301 AC XY: 22240 AN XY: 73830

African (AFR) AF: 0.608 AC: 25062 AN: 41246

American (AMR) AF: 0.267 AC: 4052 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3466

East Asian (EAS) AF: 0.441 AC: 2260 AN: 5122

South Asian (SAS) AF: 0.205 AC: 984 AN: 4794

European-Finnish (FIN) AF: 0.172 AC: 1776 AN: 10334

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10376 AN: 67780

Other (OTH) AF: 0.258 AC: 539 AN: 2090

Alfa AF: 0.239 Hom.: 796

Bravo AF: 0.329

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.29
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7252567; hg19: chr19-45878605;