rs973742

Variant names:

• chr1-158190738-G-A
• rs973742

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 0.429 in 151,846 control chromosomes in the GnomAD database, including 14,623 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 0.43 (14623 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 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: 0.429 AC: 65099 AN: 151728 Hom.: 14603 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.429 AC: 65152 AN: 151846 Hom.: 14623 Cov.: 33 AF XY: 0.432 AC XY: 32087 AN XY: 74248

African (AFR) AF: 0.336 AC: 13912 AN: 41450

American (AMR) AF: 0.357 AC: 5435 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3060 AN: 5172

South Asian (SAS) AF: 0.648 AC: 3117 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 4999 AN: 10526

Middle Eastern (MID) AF: 0.452 AC: 131 AN: 290

European-Non Finnish (NFE) AF: 0.463 AC: 31443 AN: 67864

Other (OTH) AF: 0.431 AC: 910 AN: 2112

Alfa AF: 0.437 Hom.: 2452

Bravo AF: 0.408

Asia WGS AF: 0.621 AC: 2138 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs973742; hg19: chr1-158160528;