rs7576174

Variant names:

• chr2-42091824-C-T
• rs7576174
• ENST00000743964.1:n.653-4540G>A

Variant summary

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

The ENST00000743964.1(ENSG00000296975):​n.653-4540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,126 control chromosomes in the GnomAD database, including 2,734 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 0.14 (2734 hom., cov: 32)
• Consequence: ENSG00000296975 ENST00000743964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 2 publications found

Genes affected

ENSG00000296975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374531	XR_940001.1	n.177+5793G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296975	ENST00000743964.1	n.653-4540G>A		intron_variant	Intron 1 of 1
ENSG00000296975	ENST00000743965.1	n.234-4540G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21962 AN: 152006 Hom.: 2724 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.145 AC: 22001 AN: 152126 Hom.: 2734 Cov.: 32 AF XY: 0.143 AC XY: 10642 AN XY: 74396

African (AFR) AF: 0.345 AC: 14293 AN: 41454

American (AMR) AF: 0.0720 AC: 1101 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5186

South Asian (SAS) AF: 0.122 AC: 588 AN: 4818

European-Finnish (FIN) AF: 0.0754 AC: 799 AN: 10594

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0581 AC: 3953 AN: 68000

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0847 Hom.: 1060

Bravo AF: 0.152

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.18
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7576174; hg19: chr2-42318964;