rs790896

Positions:

• chr1-237834676-A-G

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 0.674 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.672

Alfa AF: 0.636 Hom.: 8176

Bravo AF: 0.682

Asia WGS AF: 0.746 AC: 2595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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