rs1110183

Variant names:

• chr9-38456368-G-A
• rs1110183
• ENST00000635962.1:n.647+175G>A

Variant summary

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

The ENST00000685989.1(ENSG00000291061):​n.647+175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,110 control chromosomes in the GnomAD database, including 4,524 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 0.23 (4524 hom., cov: 32)
• Consequence: ENSG00000291061 ENST00000685989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 8 publications found

Genes affected

ENSG00000291061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685989.1. 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
	ENSG00000291061	ENST00000635962.1	TSL:5	n.647+175G>A		intron	N/A
	ENSG00000283162	ENST00000636076.1	TSL:6	n.76+175G>A		intron	N/A
	ENSG00000291061	ENST00000637760.3	TSL:5	n.649+175G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34855 AN: 151992 Hom.: 4517 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.229 AC: 34879 AN: 152110 Hom.: 4524 Cov.: 32 AF XY: 0.231 AC XY: 17172 AN XY: 74356

African (AFR) AF: 0.136 AC: 5648 AN: 41508

American (AMR) AF: 0.268 AC: 4101 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2882 AN: 5148

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2166 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16989 AN: 67984

Other (OTH) AF: 0.264 AC: 558 AN: 2110

Alfa AF: 0.250 Hom.: 22968

Bravo AF: 0.230

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.59
PhyloP100		-1.1

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: rs1110183;

hg19: chr9-38456365;