ENST00000707165.1:n.621+38049A>G

Variant names:

• chr2-4548208-A-G
• rs1564330
• ENST00000707165.1:n.621+38049A>G

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.621+38049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,998 control chromosomes in the GnomAD database, including 15,524 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 0.44 (15524 hom., cov: 32)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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.621+38049A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67219 AN: 151880 Hom.: 15517 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.443 AC: 67281 AN: 151998 Hom.: 15524 Cov.: 32 AF XY: 0.446 AC XY: 33132 AN XY: 74286

African (AFR) AF: 0.567 AC: 23500 AN: 41454

American (AMR) AF: 0.325 AC: 4964 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2703 AN: 5140

South Asian (SAS) AF: 0.573 AC: 2764 AN: 4824

European-Finnish (FIN) AF: 0.449 AC: 4737 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25596 AN: 67964

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.412 Hom.: 3952

Bravo AF: 0.438

Asia WGS AF: 0.586 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs1564330; hg19: chr2-4595798;