rs1698533

Variant names:

• chr14-42703075-G-A
• rs1698533
• ENST00000557251.1:n.167-30G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-42703075-G-A
• chr14-42703075-G-T

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-30G>A variant causes a intron 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: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 1 publications found

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258394	ENST00000557251.1	n.167-30G>A		intron_variant	Intron 2 of 3	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.644 AC: 26692 AN: 41450

American (AMR) AF: 0.725 AC: 11058 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2861 AN: 5160

South Asian (SAS) AF: 0.651 AC: 3134 AN: 4814

European-Finnish (FIN) AF: 0.833 AC: 8787 AN: 10554

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52401 AN: 67974

Other (OTH) AF: 0.729 AC: 1536 AN: 2106

Alfa AF: 0.745 Hom.: 52859

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1698533; hg19: chr14-43172278;