rs1034042

Variant names:

• chr9-85285179-T-C
• rs1034042
• ENST00000756340.1:n.150-907A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-85285179-T-C
• chr9-85285179-T-G

Variant summary

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

The ENST00000756340.1(ENSG00000298546):​n.150-907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,138 control chromosomes in the GnomAD database, including 16,801 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 0.44 (16801 hom., cov: 33)
• Consequence: ENSG00000298546 ENST00000756340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 2 publications found

Genes affected

ENSG00000298546 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376119	XR_930051.3	n.168-907A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298546	ENST00000756340.1	n.150-907A>G		intron_variant	Intron 2 of 2
ENSG00000298546	ENST00000756341.1	n.236-907A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67018 AN: 152020 Hom.: 16808 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.441 AC: 67019 AN: 152138 Hom.: 16801 Cov.: 33 AF XY: 0.441 AC XY: 32768 AN XY: 74346

African (AFR) AF: 0.214 AC: 8898 AN: 41506

American (AMR) AF: 0.426 AC: 6504 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1862 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1015 AN: 5180

South Asian (SAS) AF: 0.578 AC: 2781 AN: 4810

European-Finnish (FIN) AF: 0.542 AC: 5725 AN: 10568

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38557 AN: 67998

Other (OTH) AF: 0.475 AC: 1004 AN: 2114

Alfa AF: 0.461 Hom.: 2824

Bravo AF: 0.414

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1034042; hg19: chr9-87900094;