chr1-237834676-A-G

Variant names:

• chr1-237834676-A-G
• rs790896

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;