rs179562

chr14-30755252-G-Achr14-30755252-G-C

Variant summary

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

The ENST00000554665.1(ENSG00000258558):n.257-20153C>T 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 0.618 in 152,008 control chromosomes in the GnomAD database, including 32,545 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 0.62 (32545 hom., cov: 31)
• Consequence: ENST00000554665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554665.1	n.257-20153C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93884 AN: 151890 Hom.: 32549 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.618 AC: 93891 AN: 152008 Hom.: 32545 Cov.: 31 AF XY: 0.619 AC XY: 46013 AN XY: 74312

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.648

Alfa AF: 0.741 Hom.: 40968

Bravo AF: 0.587

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179562; hg19: chr14-31224458;