10-120283977-C-T

Variant names:

• chr10-120283977-C-T
• rs11199254
• ENST00000794040.1:n.116-4413C>T

Variant summary

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

The ENST00000794040.1(ENSG00000303377):​n.116-4413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 151,828 control chromosomes in the GnomAD database, including 217 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 0.020 (217 hom., cov: 32)
• Consequence: ENSG00000303377 ENST00000794040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

Genes affected

ENSG00000303377 (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 (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378515	XR_001747605.1	n.625-4413C>T		intron_variant	Intron 5 of 6
LOC105378515	XR_001747606.1	n.916-4413C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303377	ENST00000794040.1	n.116-4413C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0202 AC: 3067 AN: 151712 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.00218

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.00850

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00296

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0203 AC: 3083 AN: 151828 Hom.: 217 Cov.: 32 AF XY: 0.0240 AC XY: 1778 AN XY: 74200

African (AFR) AF: 0.00217 AC: 90 AN: 41410

American (AMR) AF: 0.0702 AC: 1073 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5168

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4814

European-Finnish (FIN) AF: 0.00850 AC: 89 AN: 10468

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00296 AC: 201 AN: 67906

Other (OTH) AF: 0.0247 AC: 52 AN: 2108

Alfa AF: 0.0119 Hom.: 37

Bravo AF: 0.0259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11199254; hg19: chr10-122043489;