rs1571379

chr14-81823593-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554814.1(ENSG00000259035):n.221-4214T>C variant causes a intron, non coding transcript 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: ENST00000554814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984704	XR_001750835.1	n.626-4214T>C		intron_variant, non_coding_transcript_variant
LOC107984704	XR_001750836.3	n.747-4214T>C		intron_variant, non_coding_transcript_variant
LOC107984704	XR_001750837.1	n.626-4214T>C		intron_variant, non_coding_transcript_variant
LOC107984704	XR_007064292.1	n.747-4214T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554814.1	n.221-4214T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.216

Alfa AF: 0.184 Hom.: 5413

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571379; hg19: chr14-82289937;