rs10494118

Variant names:

• chr1-110478293-G-C
• rs10494118
• ENST00000640695.1:n.178+4211G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-110478293-G-C
• chr1-110478293-G-T

Variant summary

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

The ENST00000640695.1(ENSG00000283999):​n.178+4211G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 152,116 control chromosomes in the GnomAD database, including 775 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 0.080 (775 hom., cov: 33)
• Consequence: ENSG00000283999 ENST00000640695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

ENSG00000283999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 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
ENSG00000283999	ENST00000640695.1	n.178+4211G>C		intron_variant	Intron 2 of 7	1

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12129 AN: 151998 Hom.: 769 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0799 AC: 12156 AN: 152116 Hom.: 775 Cov.: 33 AF XY: 0.0815 AC XY: 6062 AN XY: 74342

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0794

Alfa AF: 0.0152 Hom.: 5

Bravo AF: 0.0911

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494118; hg19: chr1-111020915;