rs7581129

Variant names:

• chr2-4619074-T-C
• rs7581129
• ENST00000707165.1:n.622-8291T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707165.1(ENSG00000291325):​n.622-8291T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,212 control chromosomes in the GnomAD database, including 749 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 0.087 (749 hom., cov: 33)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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
ENSG00000291325	ENST00000707165.1	n.622-8291T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13264 AN: 152094 Hom.: 755 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0871 AC: 13261 AN: 152212 Hom.: 749 Cov.: 33 AF XY: 0.0897 AC XY: 6672 AN XY: 74414

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0709 Hom.: 942

Bravo AF: 0.0858

Asia WGS AF: 0.219 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581129; hg19: chr2-4666664;