chr22-37434045-C-A

Variant names:

• chr22-37434045-C-A
• rs4821667
• ENST00000755882.1:n.234+1909C>A

Variant summary

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

The ENST00000755882.1(ENSG00000298484):​n.234+1909C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,066 control chromosomes in the GnomAD database, including 17,653 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 0.40 (17653 hom., cov: 32)
• Consequence: ENSG00000298484 ENST00000755882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 7 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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
ENSG00000298484	ENST00000755882.1	n.234+1909C>A		intron_variant	Intron 2 of 4
ENSG00000298484	ENST00000755883.1	n.153+1909C>A		intron_variant	Intron 1 of 4
ENSG00000298484	ENST00000755887.1	n.519-228C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60083 AN: 151948 Hom.: 17589 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.396 AC: 60199 AN: 152066 Hom.: 17653 Cov.: 32 AF XY: 0.397 AC XY: 29498 AN XY: 74330

African (AFR) AF: 0.824 AC: 34146 AN: 41448

American (AMR) AF: 0.399 AC: 6102 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5164

South Asian (SAS) AF: 0.391 AC: 1888 AN: 4828

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10586

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12776 AN: 67972

Other (OTH) AF: 0.355 AC: 750 AN: 2112

Alfa AF: 0.253 Hom.: 11758

Bravo AF: 0.426

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.2
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4821667; hg19: chr22-37830081;