rs4900109

Variant names:

• chr14-92297047-G-T
• rs4900109
• ENST00000660615.1:n.758G>T

Variant summary

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

The ENST00000660615.1(ENSG00000286630):​n.758G>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 0.32 in 152,078 control chromosomes in the GnomAD database, including 9,773 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 0.32 (9773 hom., cov: 32)
• Consequence: ENSG00000286630 ENST00000660615.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 18 publications found

Genes affected

ENSG00000286630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660615.1. 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
	ENSG00000286630	ENST00000660615.1		n.758G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307514	ENST00000826664.1		n.122-7361G>T		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.117-7361G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48686 AN: 151960 Hom.: 9770 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.320 AC: 48693 AN: 152078 Hom.: 9773 Cov.: 32 AF XY: 0.320 AC XY: 23786 AN XY: 74302

African (AFR) AF: 0.0840 AC: 3489 AN: 41536

American (AMR) AF: 0.289 AC: 4419 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1896 AN: 5172

South Asian (SAS) AF: 0.316 AC: 1523 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4844 AN: 10536

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30043 AN: 67946

Other (OTH) AF: 0.300 AC: 632 AN: 2106

Alfa AF: 0.401 Hom.: 52719

Bravo AF: 0.294

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs4900109; hg19: chr14-92763391;