3-164469007-C-T

Position:

• chr3-164469007-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000289884 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105374191	XR_001740998.2	n.290+17472C>T		intron_variant
LOC105374191	XR_001740999.3	n.290+17472C>T		intron_variant
LOC105374191	XR_001741000.2	n.290+17472C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289884	ENST00000701346.1	n.258+17472C>T		intron_variant
ENSG00000289884	ENST00000702159.1	n.290+17472C>T		intron_variant

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.484

Alfa AF: 0.338 Hom.: 831

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708486; hg19: chr3-164186795;