rs1352598

chr2-18431842-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000670548.1(ENSG00000287881):n.73+27803G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.0050 (0 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: ENST00000670548.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373454	XR_001739302.1	n.691+27803G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670548.1	n.73+27803G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 598 AN: 118652 Hom.: 0 Cov.: 26 FAILED QC

Gnomad AFR AF: 0.00276

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.00493

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.00240

Gnomad SAS AF: 0.00626

Gnomad FIN AF: 0.00118

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.00670

Gnomad OTH AF: 0.00694

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00504 AC: 598 AN: 118722 Hom.: 0 Cov.: 26 AF XY: 0.00480 AC XY: 277 AN XY: 57716

Gnomad4 AFR AF: 0.00275

Gnomad4 AMR AF: 0.00502

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.00240

Gnomad4 SAS AF: 0.00629

Gnomad4 FIN AF: 0.00118

Gnomad4 NFE AF: 0.00670

Gnomad4 OTH AF: 0.00686

Alfa AF: 0.00233 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.4
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1352598; hg19: chr2-18613108;