18-61695285-C-T

Position:

• chr18-61695285-C-T

Variant summary

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

The ENST00000590968.1(ENSG00000267175):​n.234-2012G>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 0.365 in 152,076 control chromosomes in the GnomAD database, including 13,831 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 0.37 (13831 hom., cov: 33)
• Consequence: ENST00000590968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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
	ENST00000590968.1	n.234-2012G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000590199.5	n.191-2012G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55467 AN: 151958 Hom.: 13789 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.365 AC: 55571 AN: 152076 Hom.: 13831 Cov.: 33 AF XY: 0.362 AC XY: 26890 AN XY: 74358

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.316

Alfa AF: 0.129 Hom.: 205

Bravo AF: 0.385

Asia WGS AF: 0.383 AC: 1331 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7231234; hg19: chr18-59362518;