rs7079524

Variant names:

• chr10-71309735-A-G
• rs7079524

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 0.314 in 152,152 control chromosomes in the GnomAD database, including 11,234 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 0.31 (11234 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 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: 0.314 AC: 47753 AN: 152034 Hom.: 11195 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.314 AC: 47842 AN: 152152 Hom.: 11234 Cov.: 33 AF XY: 0.312 AC XY: 23188 AN XY: 74394

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.277

Alfa AF: 0.183 Hom.: 6295

Bravo AF: 0.325

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7079524; hg19: chr10-73069492;