rs2239331

Variant names:

• chr16-22813133-G-A
• rs2239331
• ENST00000636266.2:n.942C>T

Variant summary

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

The ENST00000804049.1(ENSG00000283213):​n.228C>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: ENSG00000283213 ENST00000804049.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 7 publications found

Genes affected

ENSG00000283213 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804049.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283213	ENST00000636266.2	TSL:5	n.942C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000283213	ENST00000636354.2	TSL:5	n.222C>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000283213	ENST00000804049.1		n.228C>T		non_coding_transcript_exon	Exon 2 of 4

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

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 0.400 AC: 8 AN: 20

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.543 AC: 25 AN: 46

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.763 AC: 31594 AN: 41422

American (AMR) AF: 0.438 AC: 6694 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2136 AN: 5142

South Asian (SAS) AF: 0.471 AC: 2256 AN: 4792

European-Finnish (FIN) AF: 0.380 AC: 4005 AN: 10544

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27293 AN: 67910

Other (OTH) AF: 0.490 AC: 1033 AN: 2110

Alfa AF: 0.457 Hom.: 32846

Bravo AF: 0.522

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		0.16

Splicing

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

Other links and lift over

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