rs4900109

Positions:

• chr14-92297047-G-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000660615.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660615.1	n.758G>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.0840

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.300

Alfa AF: 0.415 Hom.: 23623

Bravo AF: 0.294

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4900109; hg19: chr14-92763391;