rs1755774

chr14-36219310-A-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, non coding transcript 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: ENST00000556542.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556542.2	n.2001+3795A>G		intron_variant, non_coding_transcript_variant		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;