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 ENST00000636266.2(ENSG00000283213):​n.942C>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 ENST00000636266.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984851	XR_001752349.2	n.285C>T		non_coding_transcript_exon_variant	Exon 2 of 4
LOC107984851	XR_005647011.2	n.1295C>T		non_coding_transcript_exon_variant	Exon 2 of 4
LOC107984851	XR_007065029.1	n.208C>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283213	ENST00000636266.2	n.942C>T		non_coding_transcript_exon_variant	Exon 1 of 2	5
ENSG00000283213	ENST00000636354.2	n.222C>T		non_coding_transcript_exon_variant	Exon 2 of 4	5
ENSG00000283213	ENST00000804049.1	n.228C>T		non_coding_transcript_exon_variant	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 v4.3

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;