rs1333914

Variant names:

• chr9-119820956-G-T
• rs1333914
• ENST00000750211.1:n.303-15216C>A

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.303-15216C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,034 control chromosomes in the GnomAD database, including 8,510 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 0.32 (8510 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 3 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. 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
	ENSG00000297691	ENST00000750211.1		n.303-15216C>A		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.385-48266C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48678 AN: 151916 Hom.: 8518 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.320 AC: 48692 AN: 152034 Hom.: 8510 Cov.: 32 AF XY: 0.319 AC XY: 23741 AN XY: 74312

African (AFR) AF: 0.169 AC: 6997 AN: 41480

American (AMR) AF: 0.315 AC: 4805 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1788 AN: 5146

South Asian (SAS) AF: 0.347 AC: 1669 AN: 4810

European-Finnish (FIN) AF: 0.347 AC: 3669 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27120 AN: 67964

Other (OTH) AF: 0.363 AC: 765 AN: 2110

Alfa AF: 0.377 Hom.: 46795

Bravo AF: 0.312

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		-0.025

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: rs1333914;

hg19: chr9-122583234;

COSMIC: COSV60399929;