14-65984535-C-T

Variant names:

• chr14-65984535-C-T
• rs1147451
• ENST00000554907.1:n.214+4035G>A

Variant summary

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

The ENST00000554907.1(ENSG00000258847):​n.214+4035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,014 control chromosomes in the GnomAD database, including 14,665 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 0.42 (14665 hom., cov: 32)
• Consequence: ENSG00000258847 ENST00000554907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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+4035G>A		intron_variant	Intron 3 of 3	2
ENSG00000258847	ENST00000775253.1	n.204+4035G>A		intron_variant	Intron 2 of 3
ENSG00000258847	ENST00000775254.1	n.203+4035G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64449 AN: 151894 Hom.: 14649 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.424 AC: 64509 AN: 152014 Hom.: 14665 Cov.: 32 AF XY: 0.425 AC XY: 31592 AN XY: 74314

African (AFR) AF: 0.589 AC: 24413 AN: 41450

American (AMR) AF: 0.399 AC: 6095 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1708 AN: 4814

European-Finnish (FIN) AF: 0.429 AC: 4531 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23549 AN: 67958

Other (OTH) AF: 0.389 AC: 820 AN: 2110

Alfa AF: 0.405 Hom.: 2021

Bravo AF: 0.429

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1147451; hg19: chr14-66451253;