rs10487524

Variant names:

• chr7-145144438-G-A
• rs10487524

Your query was ambiguous. Multiple possible variants found:

• chr7-145144438-G-A
• chr7-145144438-G-C
• chr7-145144438-G-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;