ENST00000651134.1:n.570-13747G>C

Variant names:

• chr3-157975812-C-G
• rs9856195
• ENST00000651134.1:n.570-13747G>C

Variant summary

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

The ENST00000651134.1(ENSG00000242536):​n.570-13747G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,470 control chromosomes in the GnomAD database, including 13,094 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 0.41 (13094 hom., cov: 31)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 3 publications found

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 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
ENSG00000242536	ENST00000651134.1	n.570-13747G>C		intron_variant	Intron 4 of 12

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62280 AN: 151348 Hom.: 13082 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.411 AC: 62328 AN: 151470 Hom.: 13094 Cov.: 31 AF XY: 0.411 AC XY: 30435 AN XY: 74008

African (AFR) AF: 0.334 AC: 13795 AN: 41304

American (AMR) AF: 0.389 AC: 5917 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1657 AN: 3458

East Asian (EAS) AF: 0.413 AC: 2119 AN: 5130

South Asian (SAS) AF: 0.528 AC: 2541 AN: 4812

European-Finnish (FIN) AF: 0.420 AC: 4386 AN: 10446

Middle Eastern (MID) AF: 0.424 AC: 123 AN: 290

European-Non Finnish (NFE) AF: 0.453 AC: 30736 AN: 67794

Other (OTH) AF: 0.409 AC: 859 AN: 2102

Alfa AF: 0.301 Hom.: 780

Bravo AF: 0.404

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9856195; hg19: chr3-157693601;