20-22691782-C-A

Variant names:

• chr20-22691782-C-A
• rs6137726
• ENST00000634327.1:n.497+5895C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652062.1(ENSG00000283072):​n.930+5895C>A variant causes a intron 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: ENSG00000283072 ENST00000652062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 6 publications found

Genes affected

ENSG00000283072 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652062.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283072	ENST00000634327.1	TSL:5	n.497+5895C>A		intron	N/A
	ENSG00000283072	ENST00000635654.2	TSL:5	n.424+5895C>A		intron	N/A
	ENSG00000283072	ENST00000652062.1		n.930+5895C>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.256 AC: 10632 AN: 41522

American (AMR) AF: 0.186 AC: 2840 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3472

East Asian (EAS) AF: 0.115 AC: 595 AN: 5154

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4826

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18084 AN: 67998

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.256 Hom.: 10675

Bravo AF: 0.242

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		0.77

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6137726;

hg19: chr20-22672420;