rs12535747

Variant names:

• chr7-128238282-C-A
• rs12535747
• ENST00000785131.1:n.169-16742G>T

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-16742G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,962 control chromosomes in the GnomAD database, including 7,487 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 0.30 (7487 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289434	ENST00000785131.1		n.169-16742G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45427 AN: 151844 Hom.: 7486 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.299 AC: 45443 AN: 151962 Hom.: 7487 Cov.: 32 AF XY: 0.297 AC XY: 22085 AN XY: 74270

African (AFR) AF: 0.161 AC: 6668 AN: 41410

American (AMR) AF: 0.351 AC: 5364 AN: 15274

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

East Asian (EAS) AF: 0.198 AC: 1024 AN: 5172

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4828

European-Finnish (FIN) AF: 0.343 AC: 3602 AN: 10516

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

European-Non Finnish (NFE) AF: 0.370 AC: 25123 AN: 67976

Other (OTH) AF: 0.308 AC: 652 AN: 2114

Alfa AF: 0.312 Hom.: 1189

Bravo AF: 0.298

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12535747;

hg19: chr7-127878335;