22-50671564-T-C

Variant names:

• chr22-50671564-T-C
• rs9628185
• ENST00000778025.1:n.39+3252A>G

Variant summary

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

The ENST00000778025.1(ENSG00000301328):​n.39+3252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,890 control chromosomes in the GnomAD database, including 20,284 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 0.50 (20284 hom., cov: 31)
• Consequence: ENSG00000301328 ENST00000778025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 6 publications found

Genes affected

ENSG00000301328 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778025.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301328	ENST00000778025.1		n.39+3252A>G		intron	N/A
	ENSG00000301328	ENST00000778026.1		n.41+3252A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76254 AN: 151772 Hom.: 20282 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.502 AC: 76279 AN: 151890 Hom.: 20284 Cov.: 31 AF XY: 0.492 AC XY: 36511 AN XY: 74236

African (AFR) AF: 0.637 AC: 26369 AN: 41414

American (AMR) AF: 0.397 AC: 6066 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2129 AN: 3464

East Asian (EAS) AF: 0.0858 AC: 442 AN: 5154

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4812

European-Finnish (FIN) AF: 0.454 AC: 4783 AN: 10546

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33137 AN: 67926

Other (OTH) AF: 0.514 AC: 1081 AN: 2104

Alfa AF: 0.490 Hom.: 6891

Bravo AF: 0.502

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.62
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9628185;

hg19: chr22-51109992;