rs8019707

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903318	XR_007064177.1	n.200+8A>C		splice_region_variant, intron_variant	Intron 1 of 2
LOC124903318	XR_007064178.1	n.189+19A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307927	ENST00000829887.1	n.245A>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307927	ENST00000829877.1	n.221+8A>C		splice_region_variant, intron_variant	Intron 1 of 2
ENSG00000307927	ENST00000829878.1	n.105+19A>C		intron_variant	Intron 1 of 2

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 v4.3

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;