rs72624928

Variant names:

• chr7-128410652-C-A
• rs72624928

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.125 in 152,264 control chromosomes in the GnomAD database, including 1,240 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 0.13 (1240 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.125 AC: 19035 AN: 152146 Hom.: 1238 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.125 AC: 19049 AN: 152264 Hom.: 1240 Cov.: 33 AF XY: 0.121 AC XY: 9006 AN XY: 74448

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.148

Alfa AF: 0.131 Hom.: 155

Bravo AF: 0.128

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72624928; hg19: chr7-128050706;