rs9614393

Variant names:

• chr22-44241073-T-C
• rs9614393

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 0.183 in 151,532 control chromosomes in the GnomAD database, including 2,969 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 0.18 (2969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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: 0.182 AC: 27607 AN: 151412 Hom.: 2957 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.183 AC: 27659 AN: 151532 Hom.: 2969 Cov.: 32 AF XY: 0.179 AC XY: 13292 AN XY: 74058

African (AFR) AF: 0.300 AC: 12396 AN: 41368

American (AMR) AF: 0.111 AC: 1685 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3460

East Asian (EAS) AF: 0.115 AC: 598 AN: 5178

South Asian (SAS) AF: 0.0890 AC: 427 AN: 4798

European-Finnish (FIN) AF: 0.145 AC: 1533 AN: 10538

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9738 AN: 67682

Other (OTH) AF: 0.154 AC: 322 AN: 2096

Alfa AF: 0.169 Hom.: 304

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.2
DANN	Benign	0.89
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs9614393; hg19: chr22-44636953; COSMIC: COSV66987830;