rs7582242

Variant names:

• chr2-104300696-A-G
• rs7582242
• ENST00000759000.1:n.177T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-104300696-A-G
• chr2-104300696-A-T

Variant summary

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

The ENST00000759000.1(ENSG00000298919):​n.177T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 151,908 control chromosomes in the GnomAD database, including 46,482 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 0.78 (46482 hom., cov: 30)
• Consequence: ENSG00000298919 ENST00000759000.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 publications found

Genes affected

ENSG00000298919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124908051	XR_007088651.1	n.145-2748T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298919	ENST00000759000.1	n.177T>C		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000298919	ENST00000758996.1	n.239-2748T>C		intron_variant	Intron 2 of 2
ENSG00000298919	ENST00000758997.1	n.267-2748T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117963 AN: 151790 Hom.: 46449 Cov.: 30

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.777 AC: 118048 AN: 151908 Hom.: 46482 Cov.: 30 AF XY: 0.769 AC XY: 57099 AN XY: 74238

African (AFR) AF: 0.706 AC: 29226 AN: 41372

American (AMR) AF: 0.772 AC: 11785 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2247 AN: 5152

South Asian (SAS) AF: 0.748 AC: 3601 AN: 4816

European-Finnish (FIN) AF: 0.748 AC: 7888 AN: 10546

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.846 AC: 57503 AN: 67980

Other (OTH) AF: 0.787 AC: 1654 AN: 2102

Alfa AF: 0.810 Hom.: 7905

Bravo AF: 0.775

Asia WGS AF: 0.602 AC: 2095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.50
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs7582242; hg19: chr2-104917154;