14-65981630-A-G

Variant names:

• chr14-65981630-A-G
• rs1147455
• ENST00000554907.1:n.214+6940T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000554907.1(ENSG00000258847):​n.214+6940T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,218 control chromosomes in the GnomAD database, including 6,178 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 0.28 (6178 hom., cov: 33)
• Consequence: ENSG00000258847 ENST00000554907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 4 publications found

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 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.214+6940T>C		intron_variant	Intron 3 of 3	2
ENSG00000258847	ENST00000775253.1	n.204+6940T>C		intron_variant	Intron 2 of 3
ENSG00000258847	ENST00000775254.1	n.203+6940T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42704 AN: 152100 Hom.: 6182 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.281 AC: 42720 AN: 152218 Hom.: 6178 Cov.: 33 AF XY: 0.279 AC XY: 20748 AN XY: 74424

African (AFR) AF: 0.266 AC: 11040 AN: 41534

American (AMR) AF: 0.284 AC: 4352 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 828 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1061 AN: 5182

South Asian (SAS) AF: 0.204 AC: 983 AN: 4826

European-Finnish (FIN) AF: 0.314 AC: 3330 AN: 10598

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20064 AN: 67990

Other (OTH) AF: 0.295 AC: 622 AN: 2112

Alfa AF: 0.271 Hom.: 3295

Bravo AF: 0.279

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1147455; hg19: chr14-66448348;