7-128239315-C-T

Variant names:

• chr7-128239315-C-T
• rs12536535
• ENST00000785131.1:n.169-17775G>A

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-17775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,070 control chromosomes in the GnomAD database, including 12,796 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 0.37 (12796 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 2 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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
ENSG00000289434	ENST00000785131.1	n.169-17775G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56777 AN: 151952 Hom.: 12792 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.374 AC: 56800 AN: 152070 Hom.: 12796 Cov.: 31 AF XY: 0.384 AC XY: 28536 AN XY: 74334

African (AFR) AF: 0.124 AC: 5139 AN: 41498

American (AMR) AF: 0.436 AC: 6651 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3854 AN: 5184

South Asian (SAS) AF: 0.525 AC: 2525 AN: 4812

European-Finnish (FIN) AF: 0.507 AC: 5357 AN: 10562

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30496 AN: 67960

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.263 Hom.: 783

Bravo AF: 0.354

Asia WGS AF: 0.626 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.76
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12536535; hg19: chr7-127879368;