rs11792145

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-135614139-T-A
• chr9-135614139-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000637501.1(ENSG00000236543):​n.290-1223T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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>A		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>A		intron	N/A
	ENSG00000236543	ENST00000430816.3	TSL:5 MANE Select	c.-101T>A		upstream_gene	N/A	ENSP00000490264.2	A0A1B0GUV8

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 245200 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 124328

African (AFR) AF: 0.00 AC: 0 AN: 7164

American (AMR) AF: 0.00 AC: 0 AN: 7406

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9210

East Asian (EAS) AF: 0.00 AC: 0 AN: 22872

South Asian (SAS) AF: 0.00 AC: 0 AN: 2452

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20730

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 157750

Other (OTH) AF: 0.00 AC: 0 AN: 16322

GnomAD4 genome Cov.: 35

Alfa AF: 0.00 Hom.: 95565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.54
PhyloP100		-1.9
PromoterAI		0.41	Neutral

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;