rs2423646

Positions:

• chr20-12283468-C-A
• chr20-12283468-C-G

Variant summary

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

The ENST00000654812.1(ENSG00000235292):​n.172+34582G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,902 control chromosomes in the GnomAD database, including 35,781 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 0.68 (35781 hom., cov: 31)
• Consequence: ENST00000654812.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654812.1	n.172+34582G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103069 AN: 151784 Hom.: 35721 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.648

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.679 AC: 103185 AN: 151902 Hom.: 35781 Cov.: 31 AF XY: 0.679 AC XY: 50393 AN XY: 74210

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.654

Alfa AF: 0.635 Hom.: 17440

Bravo AF: 0.685

Asia WGS AF: 0.715 AC: 2483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2423646; hg19: chr20-12264116;