rs158761

Variant names:

• chr1-22627879-C-A
• rs158761

Your query was ambiguous. Multiple possible variants found:

• chr1-22627879-C-A
• chr1-22627879-C-G

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 0.536 in 152,006 control chromosomes in the GnomAD database, including 23,586 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 0.54 (23586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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: 0.535 AC: 81300 AN: 151886 Hom.: 23533 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.536 AC: 81409 AN: 152006 Hom.: 23586 Cov.: 32 AF XY: 0.543 AC XY: 40316 AN XY: 74308

African (AFR) AF: 0.751 AC: 31152 AN: 41462

American (AMR) AF: 0.549 AC: 8393 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1448 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3049 AN: 5158

South Asian (SAS) AF: 0.640 AC: 3080 AN: 4816

European-Finnish (FIN) AF: 0.453 AC: 4793 AN: 10584

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27945 AN: 67922

Other (OTH) AF: 0.508 AC: 1070 AN: 2106

Alfa AF: 0.439 Hom.: 16535

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs158761; hg19: chr1-22954372;