rs10487524

chr7-145144438-G-A

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 0.152 in 151,942 control chromosomes in the GnomAD database, including 2,384 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 (2384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23098 AN: 151826 Hom.: 2380 Cov.: 32

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.152 AC: 23120 AN: 151942 Hom.: 2384 Cov.: 32 AF XY: 0.159 AC XY: 11820 AN XY: 74260

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.138

Alfa AF: 0.161 Hom.: 4940

Bravo AF: 0.140

Asia WGS AF: 0.398 AC: 1380 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487524; hg19: chr7-144841531;