rs9964595

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000266602	ENST00000653094.1	n.326-17105G>A		intron_variant	Intron 3 of 5
ENSG00000266602	ENST00000653330.1	n.252-17105G>A		intron_variant	Intron 2 of 4
ENSG00000266602	ENST00000655815.1	n.252-17105G>A		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.428

Alfa AF: 0.399 Hom.: 1519

Bravo AF: 0.410

Asia WGS AF: 0.522 AC: 1809 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9964595; hg19: chr18-1807674;