5-1452165-G-C

Variant names:

• chr5-1452165-G-C
• rs2078247

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 0.237 in 152,122 control chromosomes in the GnomAD database, including 4,468 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 0.24 (4468 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 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: 0.237 AC: 36033 AN: 152004 Hom.: 4453 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.237 AC: 36088 AN: 152122 Hom.: 4468 Cov.: 33 AF XY: 0.239 AC XY: 17769 AN XY: 74364

African (AFR) AF: 0.190 AC: 7902 AN: 41512

American (AMR) AF: 0.236 AC: 3607 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.141 AC: 728 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3108 AN: 10572

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18027 AN: 67974

Other (OTH) AF: 0.235 AC: 496 AN: 2108

Alfa AF: 0.129 Hom.: 227

Bravo AF: 0.227

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.97
DANN	Benign	0.86
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2078247; hg19: chr5-1452280;