rs9288111

Variant names:

• chr2-185199269-G-C
• rs9288111
• ENST00000847198.1:n.176-20385G>C

Variant summary

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

The ENST00000847198.1(ENSG00000310103):​n.176-20385G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,042 control chromosomes in the GnomAD database, including 8,304 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 0.32 (8304 hom., cov: 32)
• Consequence: ENSG00000310103 ENST00000847198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 3 publications found

Genes affected

ENSG00000310103 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847198.1. 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
	ENSG00000310103	ENST00000847198.1		n.176-20385G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 48998 AN: 150926 Hom.: 8282 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.325 AC: 49055 AN: 151042 Hom.: 8304 Cov.: 32 AF XY: 0.326 AC XY: 24031 AN XY: 73768

African (AFR) AF: 0.251 AC: 10364 AN: 41334

American (AMR) AF: 0.252 AC: 3811 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1123 AN: 3450

East Asian (EAS) AF: 0.404 AC: 2070 AN: 5122

South Asian (SAS) AF: 0.480 AC: 2311 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4091 AN: 10442

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24057 AN: 67460

Other (OTH) AF: 0.318 AC: 668 AN: 2100

Alfa AF: 0.336 Hom.: 1093

Bravo AF: 0.311

Asia WGS AF: 0.453 AC: 1552 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.015
DANN	Benign	0.48
PhyloP100		-1.7

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: rs9288111;

hg19: chr2-186063996;