rs2300573

Variant names:

• chr1-168325012-G-A
• rs2300573
• ENST00000636624.1:n.150+7366G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636624.1(ENSG00000227722):​n.150+7366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,962 control chromosomes in the GnomAD database, including 3,755 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 0.21 (3755 hom., cov: 32)
• Consequence: ENSG00000227722 ENST00000636624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

ENSG00000227722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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
ENSG00000227722	ENST00000636624.1	n.150+7366G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32552 AN: 151844 Hom.: 3749 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.214 AC: 32574 AN: 151962 Hom.: 3755 Cov.: 32 AF XY: 0.222 AC XY: 16517 AN XY: 74248

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.221

Alfa AF: 0.213 Hom.: 4666

Bravo AF: 0.211

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2300573; hg19: chr1-168294250;