rs7445013

Variant names:

• chr5-72402150-A-G
• rs7445013

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 0.472 in 152,108 control chromosomes in the GnomAD database, including 17,426 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 0.47 (17426 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 0.472 AC: 71746 AN: 151990 Hom.: 17420 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.472 AC: 71804 AN: 152108 Hom.: 17426 Cov.: 33 AF XY: 0.476 AC XY: 35408 AN XY: 74360

African (AFR) AF: 0.444 AC: 18433 AN: 41484

American (AMR) AF: 0.471 AC: 7205 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3466

East Asian (EAS) AF: 0.875 AC: 4534 AN: 5180

South Asian (SAS) AF: 0.523 AC: 2522 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5476 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30696 AN: 67988

Other (OTH) AF: 0.484 AC: 1022 AN: 2112

Alfa AF: 0.462 Hom.: 67722

Bravo AF: 0.470

Asia WGS AF: 0.677 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7445013; hg19: chr5-71697977;