ENST00000707165.1:n.506+16151A>G

Variant names:

• chr2-4467182-A-G
• rs679170
• ENST00000707165.1:n.506+16151A>G

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.506+16151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,178 control chromosomes in the GnomAD database, including 2,618 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 0.17 (2618 hom., cov: 32)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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.506+16151A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25517 AN: 152060 Hom.: 2615 Cov.: 32

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.168 AC: 25532 AN: 152178 Hom.: 2618 Cov.: 32 AF XY: 0.169 AC XY: 12552 AN XY: 74404

Gnomad4 AFR AF: 0.0526

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.190

Alfa AF: 0.189 Hom.: 493

Bravo AF: 0.169

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679170; hg19: chr2-4514772;