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. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000283999 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000283999	ENST00000420853.2	n.112+4211G>C		intron_variant	Intron 1 of 7	2
ENSG00000283999	ENST00000717017.1	n.203+4211G>C		intron_variant	Intron 2 of 8

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

African (AFR) AF: 0.149 AC: 6171 AN: 41460

American (AMR) AF: 0.132 AC: 2024 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3468

East Asian (EAS) AF: 0.162 AC: 841 AN: 5176

South Asian (SAS) AF: 0.0884 AC: 425 AN: 4806

European-Finnish (FIN) AF: 0.0357 AC: 378 AN: 10578

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0298 AC: 2029 AN: 68004

Other (OTH) AF: 0.0794 AC: 168 AN: 2116

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10494118; hg19: chr1-111020915;