rs10411016

Positions:

• chr19-7680157-G-T

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 0.606 in 152,032 control chromosomes in the GnomAD database, including 29,903 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 0.61 (29903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.606 AC: 92023 AN: 151914 Hom.: 29845 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.606 AC: 92131 AN: 152032 Hom.: 29903 Cov.: 32 AF XY: 0.600 AC XY: 44593 AN XY: 74294

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.608

Alfa AF: 0.575 Hom.: 5961

Bravo AF: 0.625

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10411016; hg19: chr19-7745043;