rs735239

chr19-7748382-A-G

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 0.264 in 152,218 control chromosomes in the GnomAD database, including 6,657 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.26 (6657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 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: 0.264 AC: 40146 AN: 152100 Hom.: 6652 Cov.: 32

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.264 AC: 40152 AN: 152218 Hom.: 6657 Cov.: 32 AF XY: 0.262 AC XY: 19490 AN XY: 74416

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.295

Alfa AF: 0.337 Hom.: 12183

Bravo AF: 0.266

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Mycobacterium tuberculosis, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.72
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735239; hg19: chr19-7813268;