rs12435895

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000258847	ENST00000775253.1	n.124-4326T>C		intron_variant	Intron 1 of 3
ENSG00000258847	ENST00000775254.1	n.123-4326T>C		intron_variant	Intron 1 of 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

African (AFR) AF: 0.153 AC: 6333 AN: 41504

American (AMR) AF: 0.225 AC: 3436 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3466

East Asian (EAS) AF: 0.141 AC: 728 AN: 5172

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4824

European-Finnish (FIN) AF: 0.272 AC: 2873 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15719 AN: 67978

Other (OTH) AF: 0.203 AC: 429 AN: 2116

Alfa AF: 0.217 Hom.: 6112

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs12435895; hg19: chr14-66459694;