rs12535708

Variant names:

• chr7-128238045-C-A
• rs12535708
• ENST00000785131.1:n.169-16505G>T

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-16505G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,132 control chromosomes in the GnomAD database, including 7,643 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 0.31 (7643 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 12 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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.169-16505G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46391 AN: 152014 Hom.: 7639 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.305 AC: 46422 AN: 152132 Hom.: 7643 Cov.: 33 AF XY: 0.303 AC XY: 22554 AN XY: 74346

African (AFR) AF: 0.182 AC: 7571 AN: 41510

American (AMR) AF: 0.355 AC: 5428 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5180

South Asian (SAS) AF: 0.293 AC: 1415 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3608 AN: 10564

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 25118 AN: 67980

Other (OTH) AF: 0.310 AC: 654 AN: 2110

Alfa AF: 0.336 Hom.: 1180

Bravo AF: 0.305

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.4
DANN	Benign	0.82
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs12535708; hg19: chr7-127878098;