3-186827530-C-T

Position:

• chr3-186827530-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702187.1(ENSG00000289971):​n.21G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,084 control chromosomes in the GnomAD database, including 15,862 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 0.45 (15862 hom., cov: 35)
• Consequence: ENST00000702187.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702187.1	n.21G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68345 AN: 151976 Hom.: 15859 Cov.: 35

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.450 AC: 68377 AN: 152084 Hom.: 15862 Cov.: 35 AF XY: 0.454 AC XY: 33730 AN XY: 74340

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.402

Alfa AF: 0.364 Hom.: 1076

Bravo AF: 0.435

Asia WGS AF: 0.479 AC: 1660 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58575091; hg19: chr3-186545319;