14-55103122-T-G

Variant names:

• chr14-55103122-T-G
• rs8019707
• ENST00000829887.1:n.245A>C

Variant summary

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

The ENST00000829887.1(ENSG00000307927):​n.245A>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 0.0626 in 152,244 control chromosomes in the GnomAD database, including 728 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 0.063 (728 hom., cov: 32)
• Consequence: ENSG00000307927 ENST00000829887.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

Genes affected

ENSG00000307927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829887.1. 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
	ENSG00000307927	ENST00000829887.1		n.245A>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000307927	ENST00000829877.1		n.221+8A>C		splice_region intron	N/A
	ENSG00000307927	ENST00000829878.1		n.105+19A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9520 AN: 152126 Hom.: 726 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00860

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0626 AC: 9536 AN: 152244 Hom.: 728 Cov.: 32 AF XY: 0.0615 AC XY: 4582 AN XY: 74448

African (AFR) AF: 0.173 AC: 7166 AN: 41508

American (AMR) AF: 0.0373 AC: 571 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3470

East Asian (EAS) AF: 0.166 AC: 860 AN: 5174

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4826

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00858 AC: 584 AN: 68026

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0312 Hom.: 60

Bravo AF: 0.0717

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs8019707; hg19: chr14-55569840;