rs735239

Variant names:

• chr19-7748382-A-G
• rs735239

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0709 AC: 2945 AN: 41560

American (AMR) AF: 0.402 AC: 6139 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.188 AC: 974 AN: 5188

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4820

European-Finnish (FIN) AF: 0.322 AC: 3402 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23679 AN: 67998

Other (OTH) AF: 0.295 AC: 624 AN: 2116

Alfa AF: 0.332 Hom.: 16095

Bravo AF: 0.266

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

ClinVar submissions

Significance: risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Mycobacterium tuberculosis, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.68
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs735239; hg19: chr19-7813268;