rs1698533

chr14-42703075-G-Achr14-42703075-G-T

Variant summary

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

The ENST00000557251.1(ENSG00000258394):n.167-30G>A 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 0.722 in 151,990 control chromosomes in the GnomAD database, including 40,085 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 0.72 (40084 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENST00000557251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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
	ENST00000557251.1	n.167-30G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109601 AN: 151870 Hom.: 40050 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.722 AC: 109693 AN: 151988 Hom.: 40084 Cov.: 32 AF XY: 0.722 AC XY: 53612 AN XY: 74254

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.729

Alfa AF: 0.749 Hom.: 40275

Bravo AF: 0.708

Asia WGS AF: 0.653 AC: 2272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	15
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1698533; hg19: chr14-43172278;