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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743964.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296975	ENST00000743964.1		n.653-4540G>A		intron	N/A
	ENSG00000296975	ENST00000743965.1		n.234-4540G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7576174;

hg19: chr2-42318964;