rs3761987

Variant names:

• chr6-14475296-A-T
• rs3761987
• ENST00000729901.1:n.1429A>T

Variant summary

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

The ENST00000729901.1(ENSG00000286277):​n.1429A>T 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 0.503 in 152,048 control chromosomes in the GnomAD database, including 20,088 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 (20088 hom., cov: 32)
• Consequence: ENSG00000286277 ENST00000729901.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 2 publications found

Genes affected

ENSG00000286277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729901.1. 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
	ENSG00000286277	ENST00000729901.1		n.1429A>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286277	ENST00000729902.1		n.1890A>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286277	ENST00000729903.1		n.1256A>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76333 AN: 151930 Hom.: 20053 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.503 AC: 76435 AN: 152048 Hom.: 20088 Cov.: 32 AF XY: 0.504 AC XY: 37449 AN XY: 74330

African (AFR) AF: 0.615 AC: 25515 AN: 41462

American (AMR) AF: 0.543 AC: 8305 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1320 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3575 AN: 5160

South Asian (SAS) AF: 0.679 AC: 3271 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3884 AN: 10572

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28901 AN: 67972

Other (OTH) AF: 0.478 AC: 1006 AN: 2106

Alfa AF: 0.462 Hom.: 2185

Bravo AF: 0.518

Asia WGS AF: 0.674 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3761987;

hg19: chr6-14475527;