18-1595020-G-A

Position:

• chr18-1595020-G-A

Variant summary

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

The ENST00000661994.1(ENSG00000266602):​n.266+28496G>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 0.713 in 151,782 control chromosomes in the GnomAD database, including 39,956 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 0.71 (39956 hom., cov: 31)
• Consequence: ENST00000661994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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
	ENST00000661994.1	n.266+28496G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108094 AN: 151666 Hom.: 39934 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.713 AC: 108155 AN: 151782 Hom.: 39956 Cov.: 31 AF XY: 0.723 AC XY: 53649 AN XY: 74174

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.718

Alfa AF: 0.764 Hom.: 32949

Bravo AF: 0.693

Asia WGS AF: 0.878 AC: 3047 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
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: rs8097348; hg19: chr18-1595021;