chr5-129129634-C-T

Variant names:

• chr5-129129634-C-T
• rs2312243

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 0.106 in 152,242 control chromosomes in the GnomAD database, including 1,057 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 0.11 (1057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.106 AC: 16153 AN: 152124 Hom.: 1054 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0565

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.106 AC: 16168 AN: 152242 Hom.: 1057 Cov.: 32 AF XY: 0.106 AC XY: 7869 AN XY: 74442

African (AFR) AF: 0.185 AC: 7687 AN: 41526

American (AMR) AF: 0.0565 AC: 864 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3472

East Asian (EAS) AF: 0.0280 AC: 145 AN: 5184

South Asian (SAS) AF: 0.0839 AC: 405 AN: 4828

European-Finnish (FIN) AF: 0.0691 AC: 733 AN: 10610

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0816 AC: 5546 AN: 68006

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0881 Hom.: 1888

Bravo AF: 0.107

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.26
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2312243; hg19: chr5-128465327;