9-21352863-C-T

Variant names:

• chr9-21352863-C-T
• rs614541

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 0.178 in 152,114 control chromosomes in the GnomAD database, including 2,543 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 (2543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.178 AC: 27102 AN: 151994 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.178 AC: 27118 AN: 152114 Hom.: 2543 Cov.: 32 AF XY: 0.180 AC XY: 13366 AN XY: 74344

African (AFR) AF: 0.161 AC: 6699 AN: 41500

American (AMR) AF: 0.240 AC: 3664 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1561 AN: 5170

South Asian (SAS) AF: 0.111 AC: 536 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2025 AN: 10582

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11377 AN: 67996

Other (OTH) AF: 0.179 AC: 376 AN: 2104

Alfa AF: 0.167 Hom.: 7185

Bravo AF: 0.183

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.32
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs614541; hg19: chr9-21352862;