rs7246355

chr19-50722987-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 0.524 in 151,918 control chromosomes in the GnomAD database, including 21,058 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 0.52 (21058 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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: 0.524 AC: 79505 AN: 151800 Hom.: 21056 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.524 AC: 79547 AN: 151918 Hom.: 21058 Cov.: 31 AF XY: 0.524 AC XY: 38937 AN XY: 74258

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.513

Alfa AF: 0.508 Hom.: 9004

Bravo AF: 0.524

Asia WGS AF: 0.465 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.0
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7246355; hg19: chr19-51226244;