chr5-149729316-C-T

Variant names:

• chr5-149729316-C-T
• rs7379457

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 0.117 in 152,032 control chromosomes in the GnomAD database, including 1,371 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 0.12 (1371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 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: 0.117 AC: 17727 AN: 151916 Hom.: 1370 Cov.: 31

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.117 AC: 17735 AN: 152032 Hom.: 1371 Cov.: 31 AF XY: 0.119 AC XY: 8858 AN XY: 74292

African (AFR) AF: 0.0280 AC: 1163 AN: 41490

American (AMR) AF: 0.232 AC: 3549 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3472

East Asian (EAS) AF: 0.0962 AC: 496 AN: 5158

South Asian (SAS) AF: 0.170 AC: 816 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10548

Middle Eastern (MID) AF: 0.145 AC: 42 AN: 290

European-Non Finnish (NFE) AF: 0.137 AC: 9300 AN: 67966

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.116 Hom.: 213

Bravo AF: 0.124

Asia WGS AF: 0.118 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.72
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs7379457; hg19: chr5-149108879;