6-22894533-C-T

Variant names:

• chr6-22894533-C-T
• rs2480006
• ENST00000420572.2:n.197+122192G>A

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.197+122192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,910 control chromosomes in the GnomAD database, including 16,148 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 0.44 (16148 hom., cov: 31)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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
ENSG00000233358	ENST00000420572.2	n.197+122192G>A		intron_variant	Intron 2 of 2	3
ENSG00000233358	ENST00000797408.1	n.332-34010G>A		intron_variant	Intron 3 of 3
ENSG00000303849	ENST00000797493.1	n.197-15118G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67484 AN: 151792 Hom.: 16101 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.445 AC: 67583 AN: 151910 Hom.: 16148 Cov.: 31 AF XY: 0.442 AC XY: 32820 AN XY: 74230

African (AFR) AF: 0.585 AC: 24217 AN: 41404

American (AMR) AF: 0.432 AC: 6591 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4132 AN: 5138

South Asian (SAS) AF: 0.409 AC: 1967 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3140 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24832 AN: 67944

Other (OTH) AF: 0.424 AC: 896 AN: 2114

Alfa AF: 0.387 Hom.: 6185

Bravo AF: 0.467

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2480006; hg19: chr6-22894762;