rs1034576

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000241921 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.737

Alfa AF: 0.765 Hom.: 25051

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034576; hg19: chr7-126063431;