14-65138010-G-T

Variant names:

• chr14-65138010-G-T
• rs17102423
• ENST00000845486.1:n.73C>A

Variant summary

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

The ENST00000845486.1(ENSG00000309915):​n.73C>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 0.381 in 152,038 control chromosomes in the GnomAD database, including 11,511 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 0.38 (11511 hom., cov: 32)
• Consequence: ENSG00000309915 ENST00000845486.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 10 publications found

Genes affected

ENSG00000309915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845486.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309915	ENST00000845486.1		n.73C>A		non_coding_transcript_exon	Exon 1 of 5
	ENSG00000309897	ENST00000845052.1		n.434-13742G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57808 AN: 151920 Hom.: 11490 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.381 AC: 57887 AN: 152038 Hom.: 11511 Cov.: 32 AF XY: 0.377 AC XY: 28049 AN XY: 74330

African (AFR) AF: 0.491 AC: 20347 AN: 41464

American (AMR) AF: 0.281 AC: 4301 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 892 AN: 3464

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5164

South Asian (SAS) AF: 0.343 AC: 1657 AN: 4824

European-Finnish (FIN) AF: 0.361 AC: 3807 AN: 10560

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24693 AN: 67964

Other (OTH) AF: 0.343 AC: 725 AN: 2114

Alfa AF: 0.361 Hom.: 36971

Bravo AF: 0.374

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.56
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs17102423; hg19: chr14-65604728;