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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725281.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294703	ENST00000725281.1		n.111+1320A>G		intron	N/A
	ENSG00000294703	ENST00000725282.1		n.68+1320A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12436689;

hg19: chr14-85654019;