rs10404257

Positions:

• chr19-38645846-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 0.502 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.514

Alfa AF: 0.554 Hom.: 3044

Bravo AF: 0.478

Asia WGS AF: 0.415 AC: 1444 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	0.39
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10404257; hg19: chr19-39136486;