rs12896399

Variant names:

• chr14-92307319-G-T
• rs12896399
• ENST00000826664.1:n.258+2775G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-92307319-G-T
• chr14-92307319-G-A

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.258+2775G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,860 control chromosomes in the GnomAD database, including 9,639 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.32 (9639 hom., cov: 31)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.30
• Publications: 117 publications found

Genes affected

ENSG00000307514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826664.1. 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
	ENSG00000307514	ENST00000826664.1		n.258+2775G>T		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.253+2775G>T		intron	N/A
	ENSG00000307514	ENST00000826666.1		n.250-1434G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48300 AN: 151740 Hom.: 9635 Cov.: 31

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.318 AC: 48306 AN: 151860 Hom.: 9639 Cov.: 31 AF XY: 0.318 AC XY: 23597 AN XY: 74188

African (AFR) AF: 0.0834 AC: 3453 AN: 41422

American (AMR) AF: 0.288 AC: 4402 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1772 AN: 5140

South Asian (SAS) AF: 0.304 AC: 1461 AN: 4806

European-Finnish (FIN) AF: 0.460 AC: 4847 AN: 10526

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29922 AN: 67926

Other (OTH) AF: 0.298 AC: 628 AN: 2108

Alfa AF: 0.399 Hom.: 57284

Bravo AF: 0.292

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	SKIN/HAIR/EYE PIGMENTATION 6, BLOND/BROWN HAIR (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.70
PhyloP100		-1.3

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: rs12896399;

hg19: chr14-92773663;