rs1642295

Positions:

• chr18-55762468-T-C

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.157-22431T>C 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 0.101 in 152,206 control chromosomes in the GnomAD database, including 1,389 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 0.10 (1389 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-22431T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654829.1	n.157-22431T>C		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.401-77T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-22431T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15367 AN: 152088 Hom.: 1387 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0789

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.101 AC: 15383 AN: 152206 Hom.: 1389 Cov.: 32 AF XY: 0.102 AC XY: 7607 AN XY: 74418

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0517

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0724 Hom.: 81

Bravo AF: 0.104

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1642295; hg19: chr18-53429699;