chr22-36137737-C-T

Position:

• chr22-36137737-C-T

Variant summary

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

The ENST00000624395.1(ENSG00000279805):​n.1614G>A 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 0.321 in 152,042 control chromosomes in the GnomAD database, including 8,046 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 0.32 (8045 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENSG00000279805 ENST00000624395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

Genes affected

ENSG00000279805 (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 (SAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36137737C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279805	ENST00000624395.1	n.1614G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48748 AN: 151916 Hom.: 8035 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.321 AC: 48794 AN: 152034 Hom.: 8045 Cov.: 32 AF XY: 0.323 AC XY: 24038 AN XY: 74318

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.295

Alfa AF: 0.348 Hom.: 16725

Bravo AF: 0.306

Asia WGS AF: 0.349 AC: 1211 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	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs132617; hg19: chr22-36533785;