rs7098825

chr10-102868477-T-C

Variant summary

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

The ENST00000636230.1(U6):n.57T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,116 control chromosomes in the GnomAD database, including 1,124 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 0.11 (1124 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: U6 ENST00000636230.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

Genes affected

U6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BORCS7-ASMT	NR_037644.1	n.407-1328T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
U6	ENST00000636230.1	n.57T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16690 AN: 151998 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.117

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.110 AC: 16715 AN: 152116 Hom.: 1124 Cov.: 32 AF XY: 0.112 AC XY: 8298 AN XY: 74370

Gnomad4 AFR AF: 0.0816

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.120

Alfa AF: 0.103 Hom.: 144

Bravo AF: 0.113

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.8
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7098825; hg19: chr10-104628234;