rs790896

Variant names:

• chr1-237834676-A-G
• rs790896

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 0.674 in 152,088 control chromosomes in the GnomAD database, including 35,522 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 0.67 (35522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.674 AC: 102454 AN: 151970 Hom.: 35476 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.674 AC: 102553 AN: 152088 Hom.: 35522 Cov.: 32 AF XY: 0.673 AC XY: 50004 AN XY: 74316

African (AFR) AF: 0.844 AC: 35013 AN: 41508

American (AMR) AF: 0.636 AC: 9714 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4071 AN: 5158

South Asian (SAS) AF: 0.630 AC: 3032 AN: 4814

European-Finnish (FIN) AF: 0.642 AC: 6771 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39892 AN: 67984

Other (OTH) AF: 0.672 AC: 1421 AN: 2114

Alfa AF: 0.623 Hom.: 47832

Bravo AF: 0.682

Asia WGS AF: 0.746 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs790896; hg19: chr1-237997976; COSMIC: COSV63674169;