chr1-117248558-A-G

Variant names:

• chr1-117248558-A-G
• rs4026198

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 0.947 in 152,044 control chromosomes in the GnomAD database, including 68,652 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 0.95 (68652 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.947 AC: 143872 AN: 151926 Hom.: 68610 Cov.: 30

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.947 AC: 143970 AN: 152044 Hom.: 68652 Cov.: 30 AF XY: 0.949 AC XY: 70517 AN XY: 74332

African (AFR) AF: 0.820 AC: 33945 AN: 41400

American (AMR) AF: 0.979 AC: 14965 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3424 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5170

South Asian (SAS) AF: 0.998 AC: 4807 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10572 AN: 10572

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67884 AN: 68010

Other (OTH) AF: 0.960 AC: 2025 AN: 2110

Alfa AF: 0.969 Hom.: 8371

Bravo AF: 0.939

Asia WGS AF: 0.989 AC: 3437 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.63
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4026198; hg19: chr1-117791180;