rs1076139

Variant names:

• chr22-35360016-G-A
• rs1076139

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 0.616 in 150,788 control chromosomes in the GnomAD database, including 30,710 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 0.62 (30710 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.615 AC: 92734 AN: 150668 Hom.: 30642 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.616 AC: 92872 AN: 150788 Hom.: 30710 Cov.: 33 AF XY: 0.615 AC XY: 45343 AN XY: 73746

African (AFR) AF: 0.855 AC: 35381 AN: 41400

American (AMR) AF: 0.662 AC: 10030 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1574 AN: 3446

East Asian (EAS) AF: 0.534 AC: 2765 AN: 5174

South Asian (SAS) AF: 0.498 AC: 2375 AN: 4770

European-Finnish (FIN) AF: 0.531 AC: 5549 AN: 10454

Middle Eastern (MID) AF: 0.479 AC: 139 AN: 290

European-Non Finnish (NFE) AF: 0.496 AC: 33292 AN: 67100

Other (OTH) AF: 0.587 AC: 1225 AN: 2088

Alfa AF: 0.531 Hom.: 37397

Bravo AF: 0.637

Asia WGS AF: 0.532 AC: 1847 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1076139; hg19: chr22-35756009;