19-38645846-G-A

Variant names:

• chr19-38645846-G-A
• rs10404257

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 0.502 in 151,788 control chromosomes in the GnomAD database, including 20,814 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 0.50 (20814 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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: 0.502 AC: 76152 AN: 151670 Hom.: 20818 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.502 AC: 76155 AN: 151788 Hom.: 20814 Cov.: 31 AF XY: 0.502 AC XY: 37242 AN XY: 74166

African (AFR) AF: 0.287 AC: 11854 AN: 41364

American (AMR) AF: 0.482 AC: 7347 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3464

East Asian (EAS) AF: 0.446 AC: 2295 AN: 5146

South Asian (SAS) AF: 0.521 AC: 2502 AN: 4802

European-Finnish (FIN) AF: 0.636 AC: 6698 AN: 10528

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.611 AC: 41487 AN: 67920

Other (OTH) AF: 0.514 AC: 1084 AN: 2108

Alfa AF: 0.543 Hom.: 3074

Bravo AF: 0.478

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10404257; hg19: chr19-39136486;