rs11190179

Variant names:

• chr10-99605556-G-A
• rs11190179
• ENST00000802583.1:n.187-5075C>T

Variant summary

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

The ENST00000802583.1(ENSG00000229278):​n.187-5075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,172 control chromosomes in the GnomAD database, including 981 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 (981 hom., cov: 32)
• Consequence: ENSG00000229278 ENST00000802583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 7 publications found

Genes affected

ENSG00000229278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802583.1. 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
	ENSG00000229278	ENST00000802583.1		n.187-5075C>T		intron	N/A
	ENSG00000229278	ENST00000802584.1		n.186-5075C>T		intron	N/A
	ENSG00000229278	ENST00000802585.1		n.168-5075C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15530 AN: 152054 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.102 AC: 15532 AN: 152172 Hom.: 981 Cov.: 32 AF XY: 0.105 AC XY: 7792 AN XY: 74390

African (AFR) AF: 0.0613 AC: 2546 AN: 41514

American (AMR) AF: 0.101 AC: 1548 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5176

South Asian (SAS) AF: 0.142 AC: 683 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1200 AN: 10570

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7377 AN: 68002

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.107 Hom.: 4181

Bravo AF: 0.100

Asia WGS AF: 0.216 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.59
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs11190179; hg19: chr10-101365313;