rs1648663

Positions:

• chr18-32543605-G-A
• chr18-32543605-G-C

Variant summary

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

The ENST00000646805.1(ENSG00000285095):​n.360-17030G>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 0.759 in 152,114 control chromosomes in the GnomAD database, including 44,826 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 0.76 (44826 hom., cov: 33)
• Consequence: ENST00000646805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646805.1	n.360-17030G>A		intron_variant, non_coding_transcript_variant
	ENST00000654761.1	n.184+25638G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115380 AN: 151996 Hom.: 44809 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.759 AC: 115435 AN: 152114 Hom.: 44826 Cov.: 33 AF XY: 0.762 AC XY: 56632 AN XY: 74354

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.777

Alfa AF: 0.813 Hom.: 70157

Bravo AF: 0.754

Asia WGS AF: 0.853 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1648663; hg19: chr18-30123568;