3-164469007-C-T

Variant names:

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

Variant summary

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

The ENST00000701346.1(ENSG00000289884):​n.258+17472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,892 control chromosomes in the GnomAD database, including 19,135 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 0.50 (19135 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374191	XR_001740998.2	n.290+17472C>T		intron_variant	Intron 1 of 3
LOC105374191	XR_001740999.3	n.290+17472C>T		intron_variant	Intron 1 of 3
LOC105374191	XR_001741000.2	n.290+17472C>T		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>T		intron_variant	Intron 1 of 5
ENSG00000289884	ENST00000702159.2	n.302+17472C>T		intron_variant	Intron 1 of 3
ENSG00000289884	ENST00000721983.1	n.84+18250C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75615 AN: 151776 Hom.: 19108 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.498 AC: 75690 AN: 151892 Hom.: 19135 Cov.: 32 AF XY: 0.498 AC XY: 36933 AN XY: 74228

African (AFR) AF: 0.574 AC: 23774 AN: 41454

American (AMR) AF: 0.552 AC: 8410 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3462

East Asian (EAS) AF: 0.345 AC: 1778 AN: 5148

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4818

European-Finnish (FIN) AF: 0.512 AC: 5380 AN: 10518

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31247 AN: 67938

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.358 Hom.: 975

Bravo AF: 0.509

Asia WGS AF: 0.359 AC: 1245 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
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;