rs12621220

Positions:

• chr2-112840678-C-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: ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623243.1	n.351C>T		non_coding_transcript_exon_variant	1/1

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;