22-39088915-C-G

Variant names:

• chr22-39088915-C-G
• rs6001423

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 0.143 in 152,218 control chromosomes in the GnomAD database, including 1,990 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 0.14 (1990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• 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 = 0.255 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: 0.143 AC: 21733 AN: 152100 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.143 AC: 21776 AN: 152218 Hom.: 1990 Cov.: 32 AF XY: 0.139 AC XY: 10332 AN XY: 74440

African (AFR) AF: 0.259 AC: 10751 AN: 41500

American (AMR) AF: 0.114 AC: 1747 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.106 AC: 546 AN: 5174

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4824

European-Finnish (FIN) AF: 0.0931 AC: 989 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0994 AC: 6760 AN: 68002

Other (OTH) AF: 0.142 AC: 300 AN: 2116

Alfa AF: 0.0294 Hom.: 24

Bravo AF: 0.152

Asia WGS AF: 0.0830 AC: 289 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	3.9
DANN	Benign	0.19
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6001423; hg19: chr22-39484920;