1-158262973-C-G

Variant names:

• chr1-158262973-C-G
• rs1230716

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 0.638 in 152,056 control chromosomes in the GnomAD database, including 33,547 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 0.64 (33547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.637 AC: 96852 AN: 151936 Hom.: 33482 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.638 AC: 96981 AN: 152056 Hom.: 33547 Cov.: 32 AF XY: 0.647 AC XY: 48053 AN XY: 74314

African (AFR) AF: 0.894 AC: 37104 AN: 41514

American (AMR) AF: 0.620 AC: 9474 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1989 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4207 AN: 5172

South Asian (SAS) AF: 0.773 AC: 3725 AN: 4822

European-Finnish (FIN) AF: 0.587 AC: 6171 AN: 10520

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32389 AN: 67950

Other (OTH) AF: 0.613 AC: 1296 AN: 2114

Alfa AF: 0.569 Hom.: 3322

Bravo AF: 0.644

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.30
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1230716; hg19: chr1-158232763;