14-105537986-T-G

Variant names:

• chr14-105537986-T-G
• rs12100587
• ENST00000760371.1:n.41A>C

Variant summary

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

The ENST00000760371.1(ENSG00000299082):​n.41A>C 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 0.2 in 152,144 control chromosomes in the GnomAD database, including 4,544 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 0.20 (4544 hom., cov: 32)
• Consequence: ENSG00000299082 ENST00000760371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 6 publications found

Genes affected

ENSG00000299082 (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 (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760371.1. 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
	ENSG00000299082	ENST00000760371.1		n.41A>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000299052	ENST00000760108.1		n.216+5467T>G		intron	N/A
	ENSG00000299052	ENST00000760109.1		n.217-4428T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30395 AN: 152026 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.200 AC: 30478 AN: 152144 Hom.: 4544 Cov.: 32 AF XY: 0.201 AC XY: 14960 AN XY: 74386

African (AFR) AF: 0.381 AC: 15786 AN: 41482

American (AMR) AF: 0.155 AC: 2375 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2584 AN: 5160

South Asian (SAS) AF: 0.191 AC: 923 AN: 4824

European-Finnish (FIN) AF: 0.0701 AC: 745 AN: 10624

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6928 AN: 67968

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.130 Hom.: 1512

Bravo AF: 0.215

Asia WGS AF: 0.316 AC: 1098 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	5.8
DANN	Benign	0.40
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs12100587; hg19: chr14-106004323;