rs2591618

Positions:

• chr19-9075497-G-A

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 0.381 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.385

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2591618; hg19: chr19-9186173;