rs11599085

Variant names:

• chr10-98286278-G-C
• rs11599085
• ENST00000793763.1:n.146+7503G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-98286278-G-C
• chr10-98286278-G-T

Variant summary

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

The ENST00000793763.1(ENSG00000303335):​n.146+7503G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,230 control chromosomes in the GnomAD database, including 6,120 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 0.26 (6120 hom., cov: 33)
• Consequence: ENSG00000303335 ENST00000793763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 2 publications found

Genes affected

ENSG00000303335 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793763.1. 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
	ENSG00000303335	ENST00000793763.1		n.146+7503G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39305 AN: 152112 Hom.: 6119 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.258 AC: 39304 AN: 152230 Hom.: 6120 Cov.: 33 AF XY: 0.252 AC XY: 18745 AN XY: 74426

African (AFR) AF: 0.108 AC: 4496 AN: 41552

American (AMR) AF: 0.245 AC: 3745 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.0768 AC: 398 AN: 5184

South Asian (SAS) AF: 0.207 AC: 999 AN: 4818

European-Finnish (FIN) AF: 0.276 AC: 2927 AN: 10604

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24730 AN: 67988

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.164 Hom.: 337

Bravo AF: 0.248

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.39
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11599085;

hg19: chr10-100046035;