rs9959449

Variant names:

• chr18-64885416-A-G
• rs9959449
• ENST00000662570.2:n.338-10332T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-64885416-A-G
• chr18-64885416-A-T

Variant summary

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

The ENST00000662570.2(ENSG00000286800):​n.338-10332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,970 control chromosomes in the GnomAD database, including 15,426 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 0.45 (15426 hom., cov: 32)
• Consequence: ENSG00000286800 ENST00000662570.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 1 publications found

Genes affected

ENSG00000286800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662570.2. 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
	ENSG00000286800	ENST00000662570.2		n.338-10332T>C		intron	N/A
	ENSG00000286800	ENST00000824051.1		n.384-10332T>C		intron	N/A
	ENSG00000286800	ENST00000824052.1		n.381-10295T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67832 AN: 151852 Hom.: 15419 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.446 AC: 67854 AN: 151970 Hom.: 15426 Cov.: 32 AF XY: 0.439 AC XY: 32638 AN XY: 74282

African (AFR) AF: 0.392 AC: 16225 AN: 41434

American (AMR) AF: 0.416 AC: 6353 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4826

European-Finnish (FIN) AF: 0.382 AC: 4026 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34532 AN: 67966

Other (OTH) AF: 0.456 AC: 959 AN: 2104

Alfa AF: 0.458 Hom.: 2659

Bravo AF: 0.443

Asia WGS AF: 0.357 AC: 1240 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9959449; hg19: chr18-62552652;