19-9075497-G-A

Variant names:

• chr19-9075497-G-A
• rs2591618

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 0.381 in 151,730 control chromosomes in the GnomAD database, including 11,530 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 0.38 (11530 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57796 AN: 151610 Hom.: 11528 Cov.: 30

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.381 AC: 57821 AN: 151730 Hom.: 11530 Cov.: 30 AF XY: 0.380 AC XY: 28189 AN XY: 74116

African (AFR) AF: 0.294 AC: 12172 AN: 41336

American (AMR) AF: 0.494 AC: 7505 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5150

South Asian (SAS) AF: 0.453 AC: 2169 AN: 4790

European-Finnish (FIN) AF: 0.332 AC: 3504 AN: 10562

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28519 AN: 67928

Other (OTH) AF: 0.385 AC: 810 AN: 2104

Alfa AF: 0.402 Hom.: 2501

Bravo AF: 0.390

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2591618; hg19: chr19-9186173;