chr19-40659347-T-G

Variant names:

• chr19-40659347-T-G
• rs7259265

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 0.198 in 152,110 control chromosomes in the GnomAD database, including 3,644 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 0.20 (3644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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: 0.198 AC: 30031 AN: 151992 Hom.: 3642 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.198 AC: 30063 AN: 152110 Hom.: 3644 Cov.: 32 AF XY: 0.195 AC XY: 14531 AN XY: 74354

African (AFR) AF: 0.332 AC: 13741 AN: 41428

American (AMR) AF: 0.127 AC: 1934 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.175 AC: 908 AN: 5186

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10006 AN: 68012

Other (OTH) AF: 0.175 AC: 371 AN: 2114

Alfa AF: 0.158 Hom.: 3251

Bravo AF: 0.203

Asia WGS AF: 0.213 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs7259265; hg19: chr19-41165252;