22-46025962-G-T

Variant names:

• chr22-46025962-G-T
• rs6519955
• ENST00000772662.1:n.197+1923C>A

Variant summary

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

The ENST00000772662.1(ENSG00000300548):​n.197+1923C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,014 control chromosomes in the GnomAD database, including 22,048 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 0.49 (22048 hom., cov: 31)
• Consequence: ENSG00000300548 ENST00000772662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 24 publications found

Genes affected

ENSG00000300548 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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
ENSG00000300548	ENST00000772662.1	n.197+1923C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74722 AN: 151896 Hom.: 21998 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.492 AC: 74820 AN: 152014 Hom.: 22048 Cov.: 31 AF XY: 0.482 AC XY: 35796 AN XY: 74302

African (AFR) AF: 0.827 AC: 34319 AN: 41490

American (AMR) AF: 0.408 AC: 6237 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3470

East Asian (EAS) AF: 0.141 AC: 725 AN: 5154

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3094 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25876 AN: 67938

Other (OTH) AF: 0.457 AC: 966 AN: 2114

Alfa AF: 0.423 Hom.: 43952

Bravo AF: 0.514

Asia WGS AF: 0.244 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6519955; hg19: chr22-46421842;