rs7256751

Variant names:

• chr19-18628687-C-T
• rs7256751

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 0.134 in 152,150 control chromosomes in the GnomAD database, including 1,683 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 (1683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.134 AC: 20337 AN: 152032 Hom.: 1679 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.134 AC: 20344 AN: 152150 Hom.: 1683 Cov.: 32 AF XY: 0.132 AC XY: 9852 AN XY: 74374

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.0729

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.107

Alfa AF: 0.126 Hom.: 239

Bravo AF: 0.132

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7256751; hg19: chr19-18739497;