rs10487140

Variant names:

• chr7-95695829-G-A
• rs10487140
• ENST00000787388.1:n.233-21278G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000787388.1(ENSG00000302505):​n.233-21278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,436 control chromosomes in the GnomAD database, including 3,096 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 0.19 (3096 hom., cov: 32)
• Consequence: ENSG00000302505 ENST00000787388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

ENSG00000302505 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375409	XR_927774.3	n.177-21278G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302505	ENST00000787388.1	n.233-21278G>A		intron_variant	Intron 2 of 3
ENSG00000302505	ENST00000787391.1	n.178-21278G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29326 AN: 151318 Hom.: 3096 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.194 AC: 29319 AN: 151436 Hom.: 3096 Cov.: 32 AF XY: 0.194 AC XY: 14346 AN XY: 73966

African (AFR) AF: 0.125 AC: 5184 AN: 41394

American (AMR) AF: 0.173 AC: 2633 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 696 AN: 3454

East Asian (EAS) AF: 0.401 AC: 2039 AN: 5088

South Asian (SAS) AF: 0.143 AC: 687 AN: 4804

European-Finnish (FIN) AF: 0.244 AC: 2568 AN: 10524

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14861 AN: 67686

Other (OTH) AF: 0.190 AC: 398 AN: 2096

Alfa AF: 0.209 Hom.: 14556

Bravo AF: 0.188

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10487140; hg19: chr7-95325141;