5-72421101-C-G

Variant names:

• chr5-72421101-C-G
• rs10515148

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 0.148 in 152,234 control chromosomes in the GnomAD database, including 1,859 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 0.15 (1859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 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: 0.148 AC: 22577 AN: 152116 Hom.: 1858 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.148 AC: 22587 AN: 152234 Hom.: 1859 Cov.: 32 AF XY: 0.151 AC XY: 11218 AN XY: 74418

African (AFR) AF: 0.108 AC: 4480 AN: 41550

American (AMR) AF: 0.195 AC: 2988 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1707 AN: 5178

South Asian (SAS) AF: 0.180 AC: 869 AN: 4830

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10586

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10137 AN: 68012

Other (OTH) AF: 0.160 AC: 338 AN: 2108

Alfa AF: 0.142 Hom.: 972

Bravo AF: 0.151

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10515148; hg19: chr5-71716928;