rs9323985

Variant names:

• chr14-98083318-T-C
• rs9323985
• ENST00000555776.1:n.122-2793A>G

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-2793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0717 in 152,160 control chromosomes in the GnomAD database, including 737 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 0.072 (737 hom., cov: 32)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 0 publications found

Genes affected

ENSG00000259097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555776.1. 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
	ENSG00000259097	ENST00000555776.1	TSL:4	n.122-2793A>G		intron	N/A
	ENSG00000259097	ENST00000663808.2		n.206-2793A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0715 AC: 10878 AN: 152042 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0717 AC: 10905 AN: 152160 Hom.: 737 Cov.: 32 AF XY: 0.0742 AC XY: 5521 AN XY: 74398

African (AFR) AF: 0.0695 AC: 2889 AN: 41540

American (AMR) AF: 0.187 AC: 2859 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1287 AN: 5142

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4822

European-Finnish (FIN) AF: 0.0532 AC: 563 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0397 AC: 2699 AN: 68006

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0623 Hom.: 164

Bravo AF: 0.0854

Asia WGS AF: 0.132 AC: 458 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.29

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: rs9323985;

hg19: chr14-98549655;