22-49287979-C-T

Variant names:

• chr22-49287979-C-T
• rs10483246
• ENST00000773840.1:n.232-1100G>A

Variant summary

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

The ENST00000773840.1(ENSG00000300754):​n.232-1100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,152 control chromosomes in the GnomAD database, including 4,810 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 0.23 (4810 hom., cov: 33)
• Consequence: ENSG00000300754 ENST00000773840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 2 publications found

Genes affected

ENSG00000300754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773840.1. 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
	ENSG00000300754	ENST00000773840.1		n.232-1100G>A		intron	N/A
	ENSG00000300754	ENST00000773841.1		n.102-1100G>A		intron	N/A
	ENSG00000300754	ENST00000773842.1		n.184-1100G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34366 AN: 152034 Hom.: 4803 Cov.: 33

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.226 AC: 34366 AN: 152152 Hom.: 4810 Cov.: 33 AF XY: 0.222 AC XY: 16545 AN XY: 74376

African (AFR) AF: 0.0622 AC: 2582 AN: 41514

American (AMR) AF: 0.256 AC: 3906 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3468

East Asian (EAS) AF: 0.162 AC: 837 AN: 5178

South Asian (SAS) AF: 0.261 AC: 1260 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2503 AN: 10582

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21184 AN: 67988

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.287 Hom.: 11120

Bravo AF: 0.218

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10483246; hg19: chr22-49683905;