rs9965495

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1	n.113+37098G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+37098G>A		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.340

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9965495; hg19: chr18-58033676;