18-2483515-A-G

Position:

• chr18-2483515-A-G

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.268+5644T>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 0.332 in 151,972 control chromosomes in the GnomAD database, including 8,628 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 0.33 (8628 hom., cov: 32)
• Consequence: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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 (AMR) allele frequency at 95% confidence interval = 0.422 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
	ENST00000639316.2	n.268+5644T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50472 AN: 151854 Hom.: 8613 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.332 AC: 50522 AN: 151972 Hom.: 8628 Cov.: 32 AF XY: 0.338 AC XY: 25128 AN XY: 74262

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.325

Alfa AF: 0.342 Hom.: 18344

Bravo AF: 0.332

Asia WGS AF: 0.320 AC: 1111 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	2.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7230412; hg19: chr18-2483514;