rs2300573

Positions:

• chr1-168325012-G-A

Variant summary

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

The ENST00000636624.1(ENSG00000293102):​n.150+7366G>A variant causes a intron, non coding transcript 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: ENST00000636624.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636624.1	n.150+7366G>A		intron_variant, non_coding_transcript_variant		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;