22-44402430-G-A

Variant names:

• chr22-44402430-G-A
• rs713756
• ENST00000777997.1:n.287+8039C>T

Variant summary

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

The ENST00000777997.1(ENSG00000301322):​n.287+8039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,282 control chromosomes in the GnomAD database, including 784 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 0.081 (784 hom., cov: 33)
• Consequence: ENSG00000301322 ENST00000777997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 3 publications found

Genes affected

ENSG00000301322 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777997.1. 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
	ENSG00000301322	ENST00000777997.1		n.287+8039C>T		intron	N/A
	ENSG00000301322	ENST00000777998.1		n.285+8039C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12378 AN: 152164 Hom.: 784 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0813 AC: 12381 AN: 152282 Hom.: 784 Cov.: 33 AF XY: 0.0825 AC XY: 6142 AN XY: 74462

African (AFR) AF: 0.0298 AC: 1238 AN: 41576

American (AMR) AF: 0.0811 AC: 1242 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 512 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1656 AN: 5164

South Asian (SAS) AF: 0.135 AC: 653 AN: 4820

European-Finnish (FIN) AF: 0.0624 AC: 662 AN: 10614

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5974 AN: 68012

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.0838 Hom.: 390

Bravo AF: 0.0832

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs713756; hg19: chr22-44798310;