chr4-10870031-A-C

Variant names:

• chr4-10870031-A-C
• rs10516213
• ENST00000775027.1:n.503-937A>C

Variant summary

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

The ENST00000775027.1(ENSG00000300906):​n.503-937A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,204 control chromosomes in the GnomAD database, including 1,466 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 0.13 (1466 hom., cov: 32)
• Consequence: ENSG00000300906 ENST00000775027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 1 publications found

Genes affected

ENSG00000300906 (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 = 0.177 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
ENSG00000300906	ENST00000775027.1	n.503-937A>C		intron_variant	Intron 1 of 2
ENSG00000300906	ENST00000775028.1	n.137-937A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20490 AN: 152086 Hom.: 1466 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.135 AC: 20491 AN: 152204 Hom.: 1466 Cov.: 32 AF XY: 0.135 AC XY: 10076 AN XY: 74402

African (AFR) AF: 0.139 AC: 5757 AN: 41514

American (AMR) AF: 0.126 AC: 1924 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3472

East Asian (EAS) AF: 0.0563 AC: 292 AN: 5190

South Asian (SAS) AF: 0.187 AC: 900 AN: 4816

European-Finnish (FIN) AF: 0.152 AC: 1616 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8763 AN: 67998

Other (OTH) AF: 0.154 AC: 326 AN: 2112

Alfa AF: 0.133 Hom.: 2639

Bravo AF: 0.132

Asia WGS AF: 0.122 AC: 427 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	2.9
DANN	Benign	0.79
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs10516213; hg19: chr4-10871655;