rs11598854

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785943.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302338	ENST00000785943.1		n.494+1876C>T		intron	N/A
	ENSG00000302338	ENST00000785944.1		n.340+2600C>T		intron	N/A
	ENSG00000302338	ENST00000785945.1		n.341+1876C>T		intron	N/A

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 v4.9

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;