rs2651090

Variant names:

• chr19-34889600-G-A
• rs2651090

Your query was ambiguous. Multiple possible variants found:

• chr19-34889600-G-A
• chr19-34889600-G-C
• chr19-34889600-G-T

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 0.0593 in 152,134 control chromosomes in the GnomAD database, including 697 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 0.059 (697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0593 AC: 9016 AN: 152016 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00943

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00919

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0593 AC: 9018 AN: 152134 Hom.: 697 Cov.: 32 AF XY: 0.0586 AC XY: 4356 AN XY: 74368

African (AFR) AF: 0.178 AC: 7361 AN: 41466

American (AMR) AF: 0.0223 AC: 341 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3470

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5182

South Asian (SAS) AF: 0.0987 AC: 475 AN: 4814

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10582

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00919 AC: 625 AN: 68014

Other (OTH) AF: 0.0464 AC: 98 AN: 2110

Alfa AF: 0.0240 Hom.: 832

Bravo AF: 0.0645

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2651090; hg19: chr19-35380504;