rs2032366

Positions:

• chr18-61599138-C-T

Variant summary

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

The ENST00000587754.1(ENSG00000267279):​n.500+9G>A 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 0.624 in 151,854 control chromosomes in the GnomAD database, including 29,815 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 0.62 (29813 hom., cov: 30)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENST00000587754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904314	XR_007066395.1	n.460+5798G>A		intron_variant, non_coding_transcript_variant
LOC124904314	XR_007066394.1	n.1814+5798G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000587754.1	n.500+9G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000590968.1	n.318-6515G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000590199.5	n.275-6515G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94726 AN: 151732 Hom.: 29787 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.624 AC: 94806 AN: 151850 Hom.: 29813 Cov.: 30 AF XY: 0.620 AC XY: 45965 AN XY: 74194

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.642

Alfa AF: 0.607 Hom.: 56735

Bravo AF: 0.630

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032366; hg19: chr18-59266371;