rs6137726

Positions:

• chr20-22691782-C-A

Variant summary

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

The ENST00000652062.1(ENSG00000283072):​n.930+5895C>A 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 0.247 in 152,146 control chromosomes in the GnomAD database, including 4,776 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 0.25 (4776 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000652062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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
	ENST00000652062.1	n.930+5895C>A		intron_variant, non_coding_transcript_variant
	ENST00000634327.1	n.497+5895C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000635654.2	n.424+5895C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37513 AN: 152028 Hom.: 4767 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.261

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.247 AC: 37557 AN: 152146 Hom.: 4776 Cov.: 33 AF XY: 0.244 AC XY: 18136 AN XY: 74352

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.257

Alfa AF: 0.260 Hom.: 7047

Bravo AF: 0.242

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	-0.84
CADD	Benign	4.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6137726; hg19: chr20-22672420;