3-194078012-A-T

Variant names:

• chr3-194078012-A-T
• rs1463697
• XM_011513352.4:c.122-200A>T

Variant summary

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

The ENST00000655827.1(ENSG00000276407):​n.61-200A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,138 control chromosomes in the GnomAD database, including 45,264 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 0.77 (45264 hom., cov: 32)
• Consequence: ENSG00000276407 ENST00000655827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898
• Publications: 4 publications found

Genes affected

LOC102724877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655827.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000276407	ENST00000615240.1	TSL:5	n.89-200A>T		intron	N/A
	ENSG00000276407	ENST00000615650.4	TSL:5	n.28-200A>T		intron	N/A
	ENSG00000276407	ENST00000655827.1		n.61-200A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116738 AN: 152020 Hom.: 45212 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.768 AC: 116849 AN: 152138 Hom.: 45264 Cov.: 32 AF XY: 0.774 AC XY: 57542 AN XY: 74372

African (AFR) AF: 0.846 AC: 35107 AN: 41508

American (AMR) AF: 0.795 AC: 12152 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2367 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4766 AN: 5192

South Asian (SAS) AF: 0.807 AC: 3882 AN: 4812

European-Finnish (FIN) AF: 0.797 AC: 8438 AN: 10592

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47773 AN: 67966

Other (OTH) AF: 0.742 AC: 1563 AN: 2106

Alfa AF: 0.743 Hom.: 5246

Bravo AF: 0.772

Asia WGS AF: 0.869 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.82
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs1463697; hg19: chr3-193795801;