chr22-42156869-C-T

Variant names:

• chr22-42156869-C-T
• rs6519313

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 0.216 in 152,114 control chromosomes in the GnomAD database, including 4,045 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 0.22 (4045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.216 AC: 32788 AN: 151996 Hom.: 4040 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.216 AC: 32792 AN: 152114 Hom.: 4045 Cov.: 32 AF XY: 0.224 AC XY: 16637 AN XY: 74346

African (AFR) AF: 0.101 AC: 4197 AN: 41516

American (AMR) AF: 0.236 AC: 3606 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1568 AN: 5176

South Asian (SAS) AF: 0.262 AC: 1264 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4077 AN: 10566

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16758 AN: 67968

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.236 Hom.: 15440

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6519313; hg19: chr22-42552875;