chr7-95695829-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787388.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302505	ENST00000787388.1		n.233-21278G>A		intron	N/A
	ENSG00000302505	ENST00000787391.1		n.178-21278G>A		intron	N/A

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 v4.9

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;