rs6134030

Variant names:

• chr20-10768251-G-T
• rs6134030
• ENST00000605292.5:n.98+95226G>T

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.98+95226G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,240 control chromosomes in the GnomAD database, including 185 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 0.036 (185 hom., cov: 32)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

ENSG00000270792 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0805 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.98+95226G>T		intron_variant	Intron 1 of 4	3
ENSG00000270792	ENST00000667822.1	n.331+95226G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5430 AN: 152122 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0357 AC: 5428 AN: 152240 Hom.: 185 Cov.: 32 AF XY: 0.0359 AC XY: 2672 AN XY: 74442

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.0277

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0151 Hom.: 35

Bravo AF: 0.0360

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.089

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6134030; hg19: chr20-10748899;