rs735239

Variant names:

• chr19-7748382-A-G
• rs735239

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Feb 01, 2006

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;