rs6122689

Positions:

• chr20-48471476-C-T

Variant summary

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

The ENST00000630976.1(ENSG00000281365):​n.169C>T 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 0.195 in 152,212 control chromosomes in the GnomAD database, including 3,125 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 0.20 (3124 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: ENST00000630976.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372645	XR_936815.3	n.135C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000630976.1	n.169C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29662 AN: 151990 Hom.: 3121 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.123 AC: 13 AN: 106 Hom.: 1 Cov.: 0 AF XY: 0.147 AC XY: 10 AN XY: 68

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.195 AC: 29680 AN: 152106 Hom.: 3124 Cov.: 32 AF XY: 0.192 AC XY: 14271 AN XY: 74364

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.0843

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.209

Alfa AF: 0.187 Hom.: 351

Bravo AF: 0.203

Asia WGS AF: 0.223 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6122689; hg19: chr20-47099722;