rs12621220

Variant names:

• chr2-112840678-C-T
• rs12621220
• ENST00000623243.1:n.351C>T

Variant summary

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

The ENST00000623243.1(ENSG00000280228):​n.351C>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 0.248 in 152,140 control chromosomes in the GnomAD database, including 5,486 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 (5485 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: ENSG00000280228 ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

ENSG00000280228 (HGNC:55634):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280228	ENST00000623243.1	n.351C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37671 AN: 151976 Hom.: 5465 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.245

GnomAD4 exome AF: 0.174 AC: 8 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.192 AC XY: 5 AN XY: 26

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.227

Gnomad4 NFE exome AF: 0.100

GnomAD4 genome AF: 0.248 AC: 37714 AN: 152094 Hom.: 5485 Cov.: 32 AF XY: 0.257 AC XY: 19098 AN XY: 74316

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.252

Alfa AF: 0.264 Hom.: 7104

Bravo AF: 0.246

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12621220; hg19: chr2-113598255; COSMIC: COSV54521330;