1-168672824-T-C

Variant names:

• chr1-168672824-T-C
• rs1538173
• ENST00000823297.1:n.305-28300T>C

Variant summary

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

The ENST00000823297.1(ENSG00000307075):​n.305-28300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,108 control chromosomes in the GnomAD database, including 45,696 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 0.77 (45696 hom., cov: 31)
• Consequence: ENSG00000307075 ENST00000823297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

Genes affected

ENSG00000307075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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
ENSG00000307075	ENST00000823297.1	n.305-28300T>C		intron_variant	Intron 1 of 1
ENSG00000307075	ENST00000823298.1	n.486-28300T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116273 AN: 151990 Hom.: 45641 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.765 AC: 116382 AN: 152108 Hom.: 45696 Cov.: 31 AF XY: 0.756 AC XY: 56224 AN XY: 74350

African (AFR) AF: 0.924 AC: 38387 AN: 41530

American (AMR) AF: 0.669 AC: 10223 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2952 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1979 AN: 5156

South Asian (SAS) AF: 0.648 AC: 3119 AN: 4814

European-Finnish (FIN) AF: 0.684 AC: 7226 AN: 10572

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50063 AN: 67964

Other (OTH) AF: 0.759 AC: 1602 AN: 2112

Alfa AF: 0.778 Hom.: 6572

Bravo AF: 0.769

Asia WGS AF: 0.585 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs1538173; hg19: chr1-168642062;