chr10-20608974-C-T

Variant names:

• chr10-20608974-C-T
• rs11598854
• ENST00000785943.1:n.494+1876C>T

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.494+1876C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,144 control chromosomes in the GnomAD database, including 1,175 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 0.10 (1175 hom., cov: 31)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 3 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376442	XR_007062080.1	n.429-887C>T		intron_variant	Intron 3 of 3
LOC105376442	XR_007062081.1	n.533-887C>T		intron_variant	Intron 3 of 3
LOC105376442	XR_930729.3	n.578-887C>T		intron_variant	Intron 3 of 3
LOC105376442	XR_930733.3	n.624-887C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302338	ENST00000785943.1	n.494+1876C>T		intron_variant	Intron 4 of 5
ENSG00000302338	ENST00000785944.1	n.340+2600C>T		intron_variant	Intron 3 of 3
ENSG00000302338	ENST00000785945.1	n.341+1876C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15914 AN: 152026 Hom.: 1174 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.105 AC: 15924 AN: 152144 Hom.: 1175 Cov.: 31 AF XY: 0.102 AC XY: 7605 AN XY: 74374

African (AFR) AF: 0.191 AC: 7920 AN: 41454

American (AMR) AF: 0.0801 AC: 1223 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3468

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5176

South Asian (SAS) AF: 0.129 AC: 620 AN: 4824

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10606

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0634 AC: 4313 AN: 68024

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0830 Hom.: 1829

Bravo AF: 0.115

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.72
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs11598854; hg19: chr10-20897903;