rs9964595

Variant names:

• chr18-1807673-G-A
• rs9964595
• ENST00000653094.1:n.326-17105G>A

Variant summary

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

The ENST00000653094.1(ENSG00000266602):​n.326-17105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,786 control chromosomes in the GnomAD database, including 12,984 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 0.41 (12984 hom., cov: 32)
• Consequence: ENSG00000266602 ENST00000653094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 2 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653094.1. 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
	ENSG00000266602	ENST00000653094.1		n.326-17105G>A		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.252-17105G>A		intron	N/A
	ENSG00000266602	ENST00000655815.1		n.252-17105G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61997 AN: 151666 Hom.: 12964 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.409 AC: 62064 AN: 151786 Hom.: 12984 Cov.: 32 AF XY: 0.413 AC XY: 30642 AN XY: 74176

African (AFR) AF: 0.376 AC: 15535 AN: 41352

American (AMR) AF: 0.438 AC: 6676 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2956 AN: 5176

South Asian (SAS) AF: 0.453 AC: 2184 AN: 4818

European-Finnish (FIN) AF: 0.464 AC: 4873 AN: 10504

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27008 AN: 67918

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.411 Hom.: 3811

Bravo AF: 0.410

Asia WGS AF: 0.522 AC: 1809 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9964595; hg19: chr18-1807674;