rs1755774

Variant names:

• chr14-36219310-A-G
• rs1755774
• ENST00000556542.2:n.2001+3795A>G

Variant summary

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

The ENST00000556542.2(ENSG00000258844):​n.2001+3795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,958 control chromosomes in the GnomAD database, including 7,003 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 0.30 (7003 hom., cov: 32)
• Consequence: ENSG00000258844 ENST00000556542.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

Genes affected

ENSG00000258844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 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
ENSG00000258844	ENST00000556542.2	n.2001+3795A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45713 AN: 151840 Hom.: 6987 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.301 AC: 45759 AN: 151958 Hom.: 7003 Cov.: 32 AF XY: 0.301 AC XY: 22326 AN XY: 74274

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.326

Alfa AF: 0.299 Hom.: 1154

Bravo AF: 0.299

Asia WGS AF: 0.426 AC: 1476 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1755774; hg19: chr14-36688516;