rs7042542

Variant names:

• chr9-121565769-T-G
• rs7042542
• ENST00000719638.1:n.257+1082A>C

Variant summary

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

The ENST00000719638.1(ENSG00000293886):​n.257+1082A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0559 in 152,104 control chromosomes in the GnomAD database, including 418 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 0.056 (418 hom., cov: 31)
• Consequence: ENSG00000293886 ENST00000719638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 2 publications found

Genes affected

ENSG00000293886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987016	XR_001746560.2	n.134+1082A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293886	ENST00000719638.1	n.257+1082A>C		intron_variant	Intron 2 of 3
ENSG00000293886	ENST00000719639.1	n.226+1082A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8476 AN: 151986 Hom.: 413 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0559 AC: 8506 AN: 152104 Hom.: 418 Cov.: 31 AF XY: 0.0557 AC XY: 4139 AN XY: 74360

African (AFR) AF: 0.130 AC: 5403 AN: 41474

American (AMR) AF: 0.0281 AC: 429 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3470

East Asian (EAS) AF: 0.0917 AC: 472 AN: 5150

South Asian (SAS) AF: 0.0495 AC: 238 AN: 4808

European-Finnish (FIN) AF: 0.0139 AC: 147 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1389 AN: 68006

Other (OTH) AF: 0.0450 AC: 95 AN: 2110

Alfa AF: 0.0462 Hom.: 28

Bravo AF: 0.0603

Asia WGS AF: 0.0660 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.33
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs7042542; hg19: chr9-124328048;