rs6134030

Positions:

• chr20-10768251-G-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, non coding transcript 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: ENST00000605292.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000605292.5	n.98+95226G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000667822.1	n.331+95226G>T		intron_variant, non_coding_transcript_variant

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;