1-161738404-T-G

Variant names:

• chr1-161738404-T-G
• rs10799941

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 0.127 in 152,190 control chromosomes in the GnomAD database, including 2,326 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 0.13 (2326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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: 0.127 AC: 19349 AN: 152072 Hom.: 2317 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.127 AC: 19384 AN: 152190 Hom.: 2326 Cov.: 32 AF XY: 0.126 AC XY: 9408 AN XY: 74418

African (AFR) AF: 0.281 AC: 11646 AN: 41482

American (AMR) AF: 0.0960 AC: 1469 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0730 AC: 253 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2336 AN: 5172

South Asian (SAS) AF: 0.0717 AC: 346 AN: 4826

European-Finnish (FIN) AF: 0.0133 AC: 141 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2922 AN: 68018

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.0676 Hom.: 816

Bravo AF: 0.145

Asia WGS AF: 0.238 AC: 827 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10799941; hg19: chr1-161708194;