1-165589988-A-G

Variant names:

• chr1-165589988-A-G
• rs952375

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 0.818 in 152,076 control chromosomes in the GnomAD database, including 51,577 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 0.82 (51577 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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: 0.818 AC: 124355 AN: 151960 Hom.: 51550 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.818 AC: 124430 AN: 152076 Hom.: 51577 Cov.: 31 AF XY: 0.820 AC XY: 60960 AN XY: 74338

African (AFR) AF: 0.669 AC: 27730 AN: 41424

American (AMR) AF: 0.805 AC: 12296 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3177 AN: 3470

East Asian (EAS) AF: 0.974 AC: 5030 AN: 5166

South Asian (SAS) AF: 0.888 AC: 4276 AN: 4818

European-Finnish (FIN) AF: 0.870 AC: 9211 AN: 10584

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59744 AN: 68010

Other (OTH) AF: 0.849 AC: 1795 AN: 2114

Alfa AF: 0.858 Hom.: 194640

Bravo AF: 0.806

Asia WGS AF: 0.905 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.59
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs952375; hg19: chr1-165559225;