rs1034576

Variant names:

• chr7-126423377-A-G
• rs1034576
• ENST00000488818.1:n.582-744A>G

Variant summary

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

The ENST00000488818.1(ENSG00000241921):​n.582-744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,048 control chromosomes in the GnomAD database, including 39,461 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 0.72 (39461 hom., cov: 31)
• Consequence: ENSG00000241921 ENST00000488818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 6 publications found

Genes affected

ENSG00000241921 (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 (AMR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241921	ENST00000488818.1	n.582-744A>G		intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108805 AN: 151930 Hom.: 39442 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.716 AC: 108864 AN: 152048 Hom.: 39461 Cov.: 31 AF XY: 0.711 AC XY: 52833 AN XY: 74300

African (AFR) AF: 0.596 AC: 24706 AN: 41482

American (AMR) AF: 0.794 AC: 12124 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2803 AN: 3466

East Asian (EAS) AF: 0.739 AC: 3805 AN: 5146

South Asian (SAS) AF: 0.719 AC: 3466 AN: 4822

European-Finnish (FIN) AF: 0.661 AC: 6987 AN: 10568

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52522 AN: 67976

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.759 Hom.: 33965

Bravo AF: 0.724

Asia WGS AF: 0.723 AC: 2511 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	0.012
DANN	Benign	0.41
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1034576; hg19: chr7-126063431;