rs2366293

Variant names:

• chr7-50188232-G-C
• rs2366293
• ENST00000774254.1:n.255+9182C>G

Variant summary

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

The ENST00000774254.1(ENSG00000300822):​n.255+9182C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,088 control chromosomes in the GnomAD database, including 53,182 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 0.84 (53182 hom., cov: 30)
• Consequence: ENSG00000300822 ENST00000774254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 7 publications found

Genes affected

ENSG00000300822 (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 = 0.947 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
ENSG00000300822	ENST00000774254.1	n.255+9182C>G		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774255.1	n.171+9182C>G		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774256.1	n.181+9182C>G		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774257.1	n.253+9182C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127057 AN: 151970 Hom.: 53139 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.836 AC: 127159 AN: 152088 Hom.: 53182 Cov.: 30 AF XY: 0.836 AC XY: 62109 AN XY: 74314

African (AFR) AF: 0.814 AC: 33758 AN: 41474

American (AMR) AF: 0.850 AC: 12991 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2515 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5019 AN: 5180

South Asian (SAS) AF: 0.771 AC: 3712 AN: 4814

European-Finnish (FIN) AF: 0.859 AC: 9066 AN: 10558

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57446 AN: 67988

Other (OTH) AF: 0.814 AC: 1720 AN: 2114

Alfa AF: 0.842 Hom.: 6703

Bravo AF: 0.836

Asia WGS AF: 0.874 AC: 3039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.32
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2366293; hg19: chr7-50227828;