ENST00000701346.1:n.258+17472C>G

Variant names:

• chr3-164469007-C-G
• rs1708486
• ENST00000701346.1:n.258+17472C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000701346.1(ENSG00000289884):​n.258+17472C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 151,956 control chromosomes in the GnomAD database, including 1 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 0.0021 (1 hom., cov: 32)
• Consequence: ENSG00000289884 ENST00000701346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

Genes affected

ENSG00000289884 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374191	XR_001740998.2	n.290+17472C>G		intron_variant	Intron 1 of 3
LOC105374191	XR_001740999.3	n.290+17472C>G		intron_variant	Intron 1 of 3
LOC105374191	XR_001741000.2	n.290+17472C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289884	ENST00000701346.1	n.258+17472C>G		intron_variant	Intron 1 of 5
ENSG00000289884	ENST00000702159.2	n.302+17472C>G		intron_variant	Intron 1 of 3
ENSG00000289884	ENST00000721983.1	n.84+18250C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.00205 AC: 312 AN: 151840 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000508

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00486

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.000760

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.00383

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

GnomAD4 genome AF: 0.00205 AC: 312 AN: 151956 Hom.: 1 Cov.: 32 AF XY: 0.00197 AC XY: 146 AN XY: 74262

African (AFR) AF: 0.000506 AC: 21 AN: 41478

American (AMR) AF: 0.00485 AC: 74 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5150

South Asian (SAS) AF: 0.000830 AC: 4 AN: 4822

European-Finnish (FIN) AF: 0.000760 AC: 8 AN: 10528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00288 AC: 196 AN: 67942

Other (OTH) AF: 0.00379 AC: 8 AN: 2112

Alfa AF: 0.000929 Hom.: 975

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.22
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1708486; hg19: chr3-164186795;