chr14-85187675-T-C

Variant names:

• chr14-85187675-T-C
• rs12436689
• ENST00000725281.1:n.111+1320A>G

Variant summary

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

The ENST00000725281.1(ENSG00000294703):​n.111+1320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,774 control chromosomes in the GnomAD database, including 3,598 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 0.19 (3598 hom., cov: 31)
• Consequence: ENSG00000294703 ENST00000725281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 8 publications found

Genes affected

ENSG00000294703 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370604	XR_944101.3	n.1595+3632A>G		intron_variant	Intron 3 of 3
LOC105370604	XR_944102.1	n.1595+3632A>G		intron_variant	Intron 3 of 3
LOC105370604	XR_944104.3	n.1472+4545A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294703	ENST00000725281.1	n.111+1320A>G		intron_variant	Intron 1 of 1
ENSG00000294703	ENST00000725282.1	n.68+1320A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29446 AN: 151656 Hom.: 3592 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.194 AC: 29465 AN: 151774 Hom.: 3598 Cov.: 31 AF XY: 0.196 AC XY: 14506 AN XY: 74146

African (AFR) AF: 0.0552 AC: 2287 AN: 41446

American (AMR) AF: 0.303 AC: 4615 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1499 AN: 5124

South Asian (SAS) AF: 0.234 AC: 1122 AN: 4802

European-Finnish (FIN) AF: 0.236 AC: 2475 AN: 10508

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15988 AN: 67898

Other (OTH) AF: 0.192 AC: 403 AN: 2098

Alfa AF: 0.211 Hom.: 4470

Bravo AF: 0.197

Asia WGS AF: 0.251 AC: 870 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.75
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs12436689; hg19: chr14-85654019;