9-135614139-T-C

Variant names:

• chr9-135614139-T-C
• rs11792145
• ENST00000637501.1:n.290-1223T>C

Variant summary

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

The ENST00000637501.1(ENSG00000236543):​n.290-1223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 397,292 control chromosomes in the GnomAD database, including 99,948 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 0.68 (35894 hom., cov: 35)
  • Exomes 𝑓: 0.72 (64054 hom.)
• Consequence: ENSG00000236543 ENST00000637501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 4 publications found

Genes affected

ENSG00000236543 (HGNC:):

LOC102723971 (HGNC:0):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637501.1. 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
	LOC102723971	NM_001375657.2	MANE Select	c.-101T>C		upstream_gene	N/A	NP_001362586.1	A0A1B0GUV8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236543	ENST00000637501.1	TSL:5	n.290-1223T>C		intron	N/A
	ENSG00000236543	ENST00000430816.3	TSL:5 MANE Select	c.-101T>C		upstream_gene	N/A	ENSP00000490264.2	A0A1B0GUV8

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103539 AN: 152074 Hom.: 35873 Cov.: 35

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.688

GnomAD4 exome AF: 0.721 AC: 176753 AN: 245100 Hom.: 64054 AF XY: 0.723 AC XY: 89834 AN XY: 124264

African (AFR) AF: 0.573 AC: 4102 AN: 7162

American (AMR) AF: 0.705 AC: 5217 AN: 7404

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 7176 AN: 9204

East Asian (EAS) AF: 0.612 AC: 13992 AN: 22864

South Asian (SAS) AF: 0.688 AC: 1683 AN: 2448

European-Finnish (FIN) AF: 0.728 AC: 15087 AN: 20724

Middle Eastern (MID) AF: 0.745 AC: 964 AN: 1294

European-Non Finnish (NFE) AF: 0.742 AC: 116954 AN: 157688

Other (OTH) AF: 0.710 AC: 11578 AN: 16312

GnomAD4 genome AF: 0.681 AC: 103614 AN: 152192 Hom.: 35894 Cov.: 35 AF XY: 0.683 AC XY: 50821 AN XY: 74404

African (AFR) AF: 0.565 AC: 23460 AN: 41510

American (AMR) AF: 0.721 AC: 11030 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2727 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5156

South Asian (SAS) AF: 0.671 AC: 3238 AN: 4826

European-Finnish (FIN) AF: 0.724 AC: 7679 AN: 10604

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50214 AN: 68000

Other (OTH) AF: 0.689 AC: 1457 AN: 2116

Alfa AF: 0.726 Hom.: 95565

Bravo AF: 0.672

Asia WGS AF: 0.628 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.33
PhyloP100		-1.9
PromoterAI		0.33	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11792145; hg19: chr9-138505985;