21-42831113-T-C

Position:

• chr21-42831113-T-C

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/exons	MANE	Protein	UniProt
		n.42831113T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225218	ENST00000431150.1	n.212A>G		non_coding_transcript_exon_variant	3/3	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;