22-19633488-C-T

Variant names:

• chr22-19633488-C-T
• rs1476445
• ENST00000420012.1:n.87G>A

Variant summary

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

The ENST00000420012.1(ENSG00000230485):​n.87G>A 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 0.543 in 154,924 control chromosomes in the GnomAD database, including 23,386 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 0.54 (22939 hom., cov: 32)
  • Exomes 𝑓: 0.55 (447 hom.)
• Consequence: ENSG00000230485 ENST00000420012.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 6 publications found

Genes affected

ENSG00000230485 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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
ENSG00000230485	ENST00000420012.1	n.87G>A		non_coding_transcript_exon_variant	Exon 1 of 3	6

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82423 AN: 151910 Hom.: 22894 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.547 AC: 1585 AN: 2896 Hom.: 447 Cov.: 0 AF XY: 0.556 AC XY: 890 AN XY: 1600

African (AFR) AF: 0.793 AC: 46 AN: 58

American (AMR) AF: 0.583 AC: 7 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 8 AN: 12

East Asian (EAS) AF: 0.717 AC: 33 AN: 46

South Asian (SAS) AF: 0.439 AC: 333 AN: 758

European-Finnish (FIN) AF: 0.598 AC: 274 AN: 458

Middle Eastern (MID) AF: 0.541 AC: 396 AN: 732

European-Non Finnish (NFE) AF: 0.594 AC: 410 AN: 690

Other (OTH) AF: 0.600 AC: 78 AN: 130

GnomAD4 genome AF: 0.543 AC: 82529 AN: 152028 Hom.: 22939 Cov.: 32 AF XY: 0.546 AC XY: 40530 AN XY: 74286

African (AFR) AF: 0.659 AC: 27326 AN: 41464

American (AMR) AF: 0.495 AC: 7562 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1755 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2624 AN: 5150

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4808

European-Finnish (FIN) AF: 0.611 AC: 6463 AN: 10580

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33149 AN: 67968

Other (OTH) AF: 0.512 AC: 1082 AN: 2112

Alfa AF: 0.507 Hom.: 87631

Bravo AF: 0.545

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.6
DANN	Benign	0.20
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1476445; hg19: chr22-19621011;