chr1-168325012-G-A

Variant names:

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

Variant summary

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

The ENST00000636624.1(ENSG00000293102):​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: ENSG00000293102 ENST00000636624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 4 publications found

Genes affected

ENSG00000293102 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000293102	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

African (AFR) AF: 0.160 AC: 6616 AN: 41440

American (AMR) AF: 0.277 AC: 4230 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1582 AN: 5154

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4816

European-Finnish (FIN) AF: 0.278 AC: 2929 AN: 10540

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14345 AN: 67970

Other (OTH) AF: 0.221 AC: 466 AN: 2106

Alfa AF: 0.213 Hom.: 6579

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
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs2300573; hg19: chr1-168294250;