21-42831113-T-C

Variant names:

• chr21-42831113-T-C
• rs2839586
• ENST00000431150.1:n.212A>G

Variant summary

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

The ENST00000431150.1(ENSG00000225218):​n.212A>G 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 0.881 in 152,282 control chromosomes in the GnomAD database, including 59,190 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 0.88 (59190 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000225218 ENST00000431150.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

ENSG00000225218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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
ENSG00000225218	ENST00000431150.1	n.212A>G		non_coding_transcript_exon_variant	Exon 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134058 AN: 152160 Hom.: 59146 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.885

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.881 AC: 134159 AN: 152278 Hom.: 59190 Cov.: 33 AF XY: 0.874 AC XY: 65108 AN XY: 74458

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.880

Alfa AF: 0.872 Hom.: 25963

Bravo AF: 0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839586; hg19: chr21-44251223;