rs10487524

Variant names:

• chr7-145144438-G-A
• rs10487524
• ENST00000788025.1:n.316-12497G>A

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000788025.1(ENSG00000302597):​n.316-12497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302597 ENST00000788025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 9 publications found

Genes affected

ENSG00000302597 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000302597	ENST00000788025.1	n.316-12497G>A		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0626 AC: 2596 AN: 41472

American (AMR) AF: 0.134 AC: 2036 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2421 AN: 5160

South Asian (SAS) AF: 0.301 AC: 1445 AN: 4804

European-Finnish (FIN) AF: 0.262 AC: 2753 AN: 10526

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10860 AN: 67968

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.156 Hom.: 7134

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10487524; hg19: chr7-144841531;