chr5-147819237-C-T

Variant names:

• chr5-147819237-C-T
• rs10515593

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 0.164 in 152,066 control chromosomes in the GnomAD database, including 2,519 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 0.16 (2519 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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: 0.164 AC: 24903 AN: 151948 Hom.: 2520 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.164 AC: 24898 AN: 152066 Hom.: 2519 Cov.: 33 AF XY: 0.165 AC XY: 12243 AN XY: 74318

African (AFR) AF: 0.0676 AC: 2806 AN: 41502

American (AMR) AF: 0.117 AC: 1788 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5184

South Asian (SAS) AF: 0.204 AC: 984 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2940 AN: 10524

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15066 AN: 67984

Other (OTH) AF: 0.159 AC: 335 AN: 2106

Alfa AF: 0.150 Hom.: 810

Bravo AF: 0.145

Asia WGS AF: 0.114 AC: 395 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.41
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs10515593; hg19: chr5-147198800;