rs9965495

Variant names:

• chr18-60366443-G-A
• rs9965495
• ENST00000650201.1:n.113+37098G>A

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+37098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,966 control chromosomes in the GnomAD database, including 10,920 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 0.36 (10920 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 8 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650201.1. 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
	ENSG00000285681	ENST00000650201.1		n.113+37098G>A		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+37098G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54641 AN: 151848 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.360 AC: 54692 AN: 151966 Hom.: 10920 Cov.: 32 AF XY: 0.351 AC XY: 26092 AN XY: 74264

African (AFR) AF: 0.532 AC: 22036 AN: 41446

American (AMR) AF: 0.308 AC: 4704 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3470

East Asian (EAS) AF: 0.131 AC: 679 AN: 5178

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2781 AN: 10542

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

European-Non Finnish (NFE) AF: 0.310 AC: 21053 AN: 67912

Other (OTH) AF: 0.340 AC: 719 AN: 2112

Alfa AF: 0.340 Hom.: 1186

Bravo AF: 0.375

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.21
PhyloP100		0.082

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: rs9965495;

hg19: chr18-58033676;