rs679170

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.91).
• 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

African (AFR) AF: 0.0526 AC: 2187 AN: 41546

American (AMR) AF: 0.232 AC: 3536 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1022 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1062 AN: 5160

South Asian (SAS) AF: 0.317 AC: 1526 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1401 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14107 AN: 68012

Other (OTH) AF: 0.190 AC: 403 AN: 2116

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs679170; hg19: chr2-4514772;