1-28873487-C-T

Variant names:

• chr1-28873487-C-T
• rs379944
• ENST00000418471.1:n.317-999G>A

Variant summary

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

The ENST00000418471.1(ENSG00000233427):​n.317-999G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,010 control chromosomes in the GnomAD database, including 1,020 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 0.11 (1020 hom., cov: 31)
• Consequence: ENSG00000233427 ENST00000418471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 5 publications found

Genes affected

ENSG00000233427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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
ENSG00000233427	ENST00000418471.1	n.317-999G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16191 AN: 151892 Hom.: 1017 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0742

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.107 AC: 16201 AN: 152010 Hom.: 1020 Cov.: 31 AF XY: 0.109 AC XY: 8064 AN XY: 74296

African (AFR) AF: 0.160 AC: 6624 AN: 41446

American (AMR) AF: 0.101 AC: 1536 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5170

South Asian (SAS) AF: 0.152 AC: 728 AN: 4804

European-Finnish (FIN) AF: 0.0815 AC: 862 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5044 AN: 67988

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.0936 Hom.: 124

Bravo AF: 0.109

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs379944; hg19: chr1-29199999;