22-37431160-C-T

Variant names:

• chr22-37431160-C-T
• rs133710
• ENST00000755887.1:n.356-814C>T

Variant summary

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

The ENST00000755887.1(ENSG00000298484):​n.356-814C>T 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 151,954 control chromosomes in the GnomAD database, including 9,836 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 (9836 hom., cov: 31)
• Consequence: ENSG00000298484 ENST00000755887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 6 publications found

Genes affected

ENSG00000298484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755887.1. 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
	ENSG00000298484	ENST00000755887.1		n.356-814C>T		intron	N/A
	ENSG00000298484	ENST00000755888.1		n.354-814C>T		intron	N/A
	ENSG00000298484	ENST00000755889.1		n.332-437C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49558 AN: 151836 Hom.: 9836 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.326 AC: 49555 AN: 151954 Hom.: 9836 Cov.: 31 AF XY: 0.324 AC XY: 24055 AN XY: 74274

African (AFR) AF: 0.104 AC: 4307 AN: 41488

American (AMR) AF: 0.310 AC: 4730 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1492 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1383 AN: 5158

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4774 AN: 10554

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30230 AN: 67894

Other (OTH) AF: 0.352 AC: 742 AN: 2106

Alfa AF: 0.413 Hom.: 18779

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs133710; hg19: chr22-37827196;