chr1-118312964-A-G

Variant names:

• chr1-118312964-A-G
• rs9428104

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 0.736 in 150,726 control chromosomes in the GnomAD database, including 40,931 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 0.74 (40931 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 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: 0.736 AC: 110791 AN: 150612 Hom.: 40883 Cov.: 25

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.736 AC: 110896 AN: 150726 Hom.: 40931 Cov.: 25 AF XY: 0.736 AC XY: 54107 AN XY: 73520

African (AFR) AF: 0.720 AC: 29530 AN: 40990

American (AMR) AF: 0.736 AC: 11117 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2361 AN: 3458

East Asian (EAS) AF: 0.635 AC: 3222 AN: 5074

South Asian (SAS) AF: 0.689 AC: 3282 AN: 4760

European-Finnish (FIN) AF: 0.771 AC: 7994 AN: 10364

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 50873 AN: 67702

Other (OTH) AF: 0.755 AC: 1561 AN: 2068

Alfa AF: 0.822 Hom.: 70728

Bravo AF: 0.733

Asia WGS AF: 0.686 AC: 2387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.96
DANN	Benign	0.10
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9428104; hg19: chr1-118855587;