20-19019182-G-T

Position:

• chr20-19019182-G-T

Variant summary

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

The ENST00000617956.1(ENSG00000274863):​n.470-8666C>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 0.639 in 152,022 control chromosomes in the GnomAD database, including 31,401 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 0.64 (31401 hom., cov: 32)
• Consequence: ENST00000617956.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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 = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000617956.1	n.470-8666C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96980 AN: 151904 Hom.: 31338 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.639 AC: 97106 AN: 152022 Hom.: 31401 Cov.: 32 AF XY: 0.648 AC XY: 48171 AN XY: 74334

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.621

Alfa AF: 0.607 Hom.: 51204

Bravo AF: 0.636

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
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: rs6045766; hg19: chr20-18999826;