5-170136363-T-C

Variant names:

• chr5-170136363-T-C
• rs12515896

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 0.666 in 152,006 control chromosomes in the GnomAD database, including 35,692 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 0.67 (35692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.52
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101141 AN: 151888 Hom.: 35685 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.666 AC: 101175 AN: 152006 Hom.: 35692 Cov.: 31 AF XY: 0.665 AC XY: 49429 AN XY: 74296

African (AFR) AF: 0.419 AC: 17347 AN: 41416

American (AMR) AF: 0.740 AC: 11311 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2793 AN: 3462

East Asian (EAS) AF: 0.499 AC: 2568 AN: 5144

South Asian (SAS) AF: 0.727 AC: 3505 AN: 4822

European-Finnish (FIN) AF: 0.729 AC: 7716 AN: 10580

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53706 AN: 67980

Other (OTH) AF: 0.690 AC: 1460 AN: 2116

Alfa AF: 0.753 Hom.: 168285

Bravo AF: 0.656

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.054
DANN	Benign	0.51
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs12515896; hg19: chr5-169563367;