22-46147582-T-C

Variant names:

• chr22-46147582-T-C
• rs135556
• ENST00000846710.1:n.328+3485A>G

Variant summary

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

The ENST00000846710.1(ENSG00000310037):​n.328+3485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,040 control chromosomes in the GnomAD database, including 9,309 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 0.33 (9309 hom., cov: 32)
• Consequence: ENSG00000310037 ENST00000846710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 7 publications found

Genes affected

ENSG00000310037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310037	ENST00000846710.1		n.328+3485A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49452 AN: 151920 Hom.: 9280 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.326 AC: 49532 AN: 152040 Hom.: 9309 Cov.: 32 AF XY: 0.319 AC XY: 23679 AN XY: 74322

African (AFR) AF: 0.511 AC: 21164 AN: 41446

American (AMR) AF: 0.219 AC: 3347 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.0824 AC: 426 AN: 5170

South Asian (SAS) AF: 0.159 AC: 765 AN: 4826

European-Finnish (FIN) AF: 0.257 AC: 2716 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19425 AN: 67960

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.316 Hom.: 1007

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.0050
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs135556; hg19: chr22-46543485;