rs1476029

Variant names:

• chr22-36121884-C-T
• rs1476029

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 0.102 in 152,038 control chromosomes in the GnomAD database, including 987 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 0.10 (987 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 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: 0.102 AC: 15511 AN: 151920 Hom.: 987 Cov.: 31

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.102 AC: 15511 AN: 152038 Hom.: 987 Cov.: 31 AF XY: 0.0996 AC XY: 7401 AN XY: 74292

African (AFR) AF: 0.0284 AC: 1176 AN: 41478

American (AMR) AF: 0.0783 AC: 1196 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5178

South Asian (SAS) AF: 0.101 AC: 488 AN: 4816

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10562

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10502 AN: 67954

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.128 Hom.: 1881

Bravo AF: 0.0964

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.82
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1476029; hg19: chr22-36517932;