rs1034576

Positions:

• chr7-126423377-A-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, non coding transcript 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: ENST00000488818.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000488818.1	n.582-744A>G		intron_variant, non_coding_transcript_variant		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;