chr1-161738404-T-G

Variant names:

• chr1-161738404-T-G
• rs10799941

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 0.127 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.0960

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.0717

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0430

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0557 Hom.: 403

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10799941; hg19: chr1-161708194;