chr3-192087371-T-C

Variant names:

• chr3-192087371-T-C
• rs1602517
• ENST00000653109.1:n.125-6930A>G

Variant summary

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

The ENST00000653109.1(ENSG00000287178):​n.125-6930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,800 control chromosomes in the GnomAD database, including 27,361 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 0.57 (27361 hom., cov: 31)
• Consequence: ENSG00000287178 ENST00000653109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 4 publications found

Genes affected

ENSG00000287178 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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
ENSG00000287178	ENST00000653109.1	n.125-6930A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86564 AN: 151682 Hom.: 27343 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.570 AC: 86601 AN: 151800 Hom.: 27361 Cov.: 31 AF XY: 0.575 AC XY: 42682 AN XY: 74212

African (AFR) AF: 0.274 AC: 11350 AN: 41446

American (AMR) AF: 0.684 AC: 10434 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2248 AN: 3464

East Asian (EAS) AF: 0.802 AC: 4140 AN: 5164

South Asian (SAS) AF: 0.557 AC: 2679 AN: 4812

European-Finnish (FIN) AF: 0.697 AC: 7350 AN: 10538

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46347 AN: 67808

Other (OTH) AF: 0.591 AC: 1239 AN: 2098

Alfa AF: 0.645 Hom.: 106512

Bravo AF: 0.561

Asia WGS AF: 0.639 AC: 2219 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1602517; hg19: chr3-191805160;