ENST00000707165.1:n.622-8291T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707165.1. 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
	ENSG00000291325	ENST00000707165.1		n.622-8291T>C		intron	N/A

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

African (AFR) AF: 0.113 AC: 4702 AN: 41534

American (AMR) AF: 0.0596 AC: 911 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3466

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5156

South Asian (SAS) AF: 0.204 AC: 986 AN: 4822

European-Finnish (FIN) AF: 0.0491 AC: 521 AN: 10606

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0614 AC: 4175 AN: 68014

Other (OTH) AF: 0.0874 AC: 185 AN: 2116

Alfa AF: 0.0727 Hom.: 2075

Bravo AF: 0.0858

Asia WGS AF: 0.219 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7581129; hg19: chr2-4666664;