chr20-10953559-C-T

Variant names:

• chr20-10953559-C-T
• rs6104678
• ENST00000605292.5:n.440-38039C>T

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.440-38039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,036 control chromosomes in the GnomAD database, including 1,793 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 0.15 (1793 hom., cov: 32)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

Genes affected

ENSG00000270792 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270792	ENST00000605292.5	n.440-38039C>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22916 AN: 151918 Hom.: 1791 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.151 AC: 22931 AN: 152036 Hom.: 1793 Cov.: 32 AF XY: 0.145 AC XY: 10806 AN XY: 74308

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.166

Alfa AF: 0.164 Hom.: 3144

Bravo AF: 0.154

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.87
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6104678; hg19: chr20-10934207;