rs12435895

Variant names:

• chr14-65992976-A-G
• rs12435895
• ENST00000554907.1:n.70-3233T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554907.1(ENSG00000258847):​n.70-3233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,140 control chromosomes in the GnomAD database, including 3,374 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 0.20 (3374 hom., cov: 32)
• Consequence: ENSG00000258847 ENST00000554907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258847	ENST00000554907.1	n.70-3233T>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30790 AN: 152022 Hom.: 3376 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.202 AC: 30797 AN: 152140 Hom.: 3374 Cov.: 32 AF XY: 0.200 AC XY: 14901 AN XY: 74388

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0989

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.203

Alfa AF: 0.218 Hom.: 4862

Bravo AF: 0.200

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.065
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12435895; hg19: chr14-66459694;