rs2239331

chr16-22813133-G-A

Variant summary

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

The ENST00000636354.1(ENSG00000283213):n.69C>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 0.505 in 151,938 control chromosomes in the GnomAD database, including 21,410 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 0.50 (21399 hom., cov: 30)
  • Exomes 𝑓: 0.49 (11 hom.)
• Consequence: ENST00000636354.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984851	XR_001752349.2	n.285C>T		non_coding_transcript_exon_variant	2/4
LOC107984851	XR_005647011.2	n.1295C>T		non_coding_transcript_exon_variant	2/4
LOC107984851	XR_007065029.1	n.208C>T		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636354.1	n.69C>T		non_coding_transcript_exon_variant	1/3	5
	ENST00000636266.1	n.548C>T		non_coding_transcript_exon_variant	1/2	5

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76593 AN: 151746 Hom.: 21369 Cov.: 30

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.486 AC: 36 AN: 74 Hom.: 11 Cov.: 0 AF XY: 0.457 AC XY: 21 AN XY: 46

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.543

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.505 AC: 76674 AN: 151864 Hom.: 21399 Cov.: 30 AF XY: 0.502 AC XY: 37270 AN XY: 74214

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.490

Alfa AF: 0.426 Hom.: 19032

Bravo AF: 0.522

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2239331; hg19: chr16-22824454; COSMIC: COSV54458051;