5-132672519-T-C

Variant names:

• chr5-132672519-T-C
• rs10058157

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 0.0548 in 145,440 control chromosomes in the GnomAD database, including 570 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 0.055 (570 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.0548 AC: 7968 AN: 145330 Hom.: 568 Cov.: 26

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00112

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.00206

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0143

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0548 AC: 7975 AN: 145440 Hom.: 570 Cov.: 26 AF XY: 0.0539 AC XY: 3818 AN XY: 70866

African (AFR) AF: 0.153 AC: 5909 AN: 38542

American (AMR) AF: 0.0307 AC: 448 AN: 14600

Ashkenazi Jewish (ASJ) AF: 0.00206 AC: 7 AN: 3392

East Asian (EAS) AF: 0.117 AC: 587 AN: 5028

South Asian (SAS) AF: 0.0279 AC: 124 AN: 4450

European-Finnish (FIN) AF: 0.0131 AC: 132 AN: 10060

Middle Eastern (MID) AF: 0.0152 AC: 4 AN: 264

European-Non Finnish (NFE) AF: 0.0101 AC: 666 AN: 66224

Other (OTH) AF: 0.0488 AC: 97 AN: 1988

Alfa AF: 0.000784 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.71
DANN	Benign	0.38
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10058157; hg19: chr5-132008211;