rs2423646

Variant names:

• chr20-12283468-C-A
• rs2423646
• ENST00000654812.1:n.172+34582G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654812.1(ENSG00000235292):​n.172+34582G>T variant causes a intron 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: ENSG00000235292 ENST00000654812.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 4 publications found

Genes affected

ENSG00000235292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235292	ENST00000654812.1	n.172+34582G>T		intron_variant	Intron 1 of 2
ENSG00000235292	ENST00000728195.1	n.175+34582G>T		intron_variant	Intron 1 of 2
ENSG00000235292	ENST00000728196.1	n.221+34518G>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.838 AC: 34722 AN: 41458

American (AMR) AF: 0.648 AC: 9877 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1809 AN: 3464

East Asian (EAS) AF: 0.682 AC: 3507 AN: 5140

South Asian (SAS) AF: 0.668 AC: 3215 AN: 4810

European-Finnish (FIN) AF: 0.642 AC: 6759 AN: 10536

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41314 AN: 67934

Other (OTH) AF: 0.654 AC: 1379 AN: 2110

Alfa AF: 0.640 Hom.: 66261

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2423646; hg19: chr20-12264116;