chr1-199996040-G-A

Variant names:

• chr1-199996040-G-A
• rs10919791

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 0.233 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.113 AC: 4666 AN: 41378

American (AMR) AF: 0.303 AC: 4597 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3471 AN: 5110

South Asian (SAS) AF: 0.443 AC: 2127 AN: 4802

European-Finnish (FIN) AF: 0.365 AC: 3829 AN: 10478

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15189 AN: 67922

Other (OTH) AF: 0.221 AC: 464 AN: 2104

Alfa AF: 0.227 Hom.: 14194

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10919791; hg19: chr1-199965168;