rs7252567

Positions:

• chr19-45375347-C-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 0.303 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.258

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7252567; hg19: chr19-45878605;