rs62132295

Variant names:

• chr19-840448-G-A
• rs62132295

Your query was ambiguous. Multiple possible variants found:

• chr19-840448-G-A
• chr19-840448-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 0.259 in 132,144 control chromosomes in the GnomAD database, including 4,669 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 0.26 (4669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 34254 AN: 132030 Hom.: 4667 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.259 AC: 34271 AN: 132144 Hom.: 4669 Cov.: 31 AF XY: 0.260 AC XY: 16705 AN XY: 64354

African (AFR) AF: 0.121 AC: 4253 AN: 35052

American (AMR) AF: 0.209 AC: 2616 AN: 12496

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 829 AN: 3096

East Asian (EAS) AF: 0.166 AC: 758 AN: 4578

South Asian (SAS) AF: 0.130 AC: 531 AN: 4100

European-Finnish (FIN) AF: 0.409 AC: 3808 AN: 9314

Middle Eastern (MID) AF: 0.377 AC: 95 AN: 252

European-Non Finnish (NFE) AF: 0.342 AC: 20731 AN: 60704

Other (OTH) AF: 0.272 AC: 486 AN: 1784

Alfa AF: 0.177 Hom.: 511

Bravo AF: 0.207

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.65
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs62132295; hg19: chr19-840448;