22-35016843-T-C

Variant names:

• chr22-35016843-T-C
• rs2008519

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 0.466 in 151,948 control chromosomes in the GnomAD database, including 17,212 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 0.47 (17212 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70829 AN: 151830 Hom.: 17196 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.466 AC: 70875 AN: 151948 Hom.: 17212 Cov.: 31 AF XY: 0.459 AC XY: 34092 AN XY: 74300

African (AFR) AF: 0.356 AC: 14727 AN: 41412

American (AMR) AF: 0.565 AC: 8620 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1872 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1366 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1489 AN: 4804

European-Finnish (FIN) AF: 0.460 AC: 4857 AN: 10560

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36190 AN: 67962

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.511 Hom.: 53679

Bravo AF: 0.474

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.55
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2008519; hg19: chr22-35412833;