18-51026855-C-G

Position:

• chr18-51026855-C-G

Variant summary

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

The ENST00000701227.1(ENSG00000289868):​n.133+3063G>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 0.424 in 152,018 control chromosomes in the GnomAD database, including 13,793 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 0.42 (13793 hom., cov: 32)
• Consequence: ENST00000701227.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

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 = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985152	XR_007066370.1	n.177+3063G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701227.1	n.133+3063G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64326 AN: 151900 Hom.: 13776 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.424 AC: 64406 AN: 152018 Hom.: 13793 Cov.: 32 AF XY: 0.421 AC XY: 31271 AN XY: 74308

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.442

Alfa AF: 0.394 Hom.: 1484

Bravo AF: 0.435

Asia WGS AF: 0.384 AC: 1333 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	0.81
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939650; hg19: chr18-48553225;