chr14-81823593-T-C

Variant names:

• chr14-81823593-T-C
• rs1571379
• ENST00000554814.1:n.221-4214T>C

Variant summary

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

The ENST00000554814.1(ENSG00000259035):​n.221-4214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,014 control chromosomes in the GnomAD database, including 3,872 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 0.22 (3872 hom., cov: 31)
• Consequence: ENSG00000259035 ENST00000554814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 4 publications found

Genes affected

ENSG00000259035 (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 (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984704	XR_001750835.1	n.626-4214T>C		intron_variant	Intron 2 of 3
LOC107984704	XR_001750836.3	n.747-4214T>C		intron_variant	Intron 2 of 3
LOC107984704	XR_001750837.1	n.626-4214T>C		intron_variant	Intron 2 of 3
LOC107984704	XR_007064292.1	n.747-4214T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259035	ENST00000554814.1	n.221-4214T>C		intron_variant	Intron 2 of 3	4
ENSG00000259035	ENST00000661287.1	n.177-4214T>C		intron_variant	Intron 2 of 3
ENSG00000259035	ENST00000662303.1	n.370-4214T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33507 AN: 151896 Hom.: 3867 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.221 AC: 33537 AN: 152014 Hom.: 3872 Cov.: 31 AF XY: 0.226 AC XY: 16814 AN XY: 74308

African (AFR) AF: 0.262 AC: 10873 AN: 41470

American (AMR) AF: 0.258 AC: 3939 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3466

East Asian (EAS) AF: 0.305 AC: 1582 AN: 5180

South Asian (SAS) AF: 0.227 AC: 1087 AN: 4790

European-Finnish (FIN) AF: 0.256 AC: 2707 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12151 AN: 67948

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.189 Hom.: 11752

Bravo AF: 0.221

Asia WGS AF: 0.292 AC: 1016 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	3.4
DANN	Benign	0.74
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1571379; hg19: chr14-82289937;