rs1571379

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554814.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259035	ENST00000554814.1	TSL:4	n.221-4214T>C		intron	N/A
	ENSG00000259035	ENST00000661287.1		n.177-4214T>C		intron	N/A
	ENSG00000259035	ENST00000662303.1		n.370-4214T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1571379;

hg19: chr14-82289937;