rs10919791

chr1-199996040-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 0.233 in 151,650 control chromosomes in the GnomAD database, including 5,296 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 0.23 (5296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.234 AC: 35392 AN: 151532 Hom.: 5292 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.233 AC: 35391 AN: 151650 Hom.: 5296 Cov.: 31 AF XY: 0.247 AC XY: 18322 AN XY: 74058

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.221

Alfa AF: 0.226 Hom.: 5869

Bravo AF: 0.223

Asia WGS AF: 0.493 AC: 1711 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	0.60
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10919791; hg19: chr1-199965168;