rs9306906

Variant names:

• chr4-33964745-C-T
• rs9306906
• ENST00000505018.1:n.307+6046G>A

Variant summary

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

The ENST00000505018.1(ENSG00000250954):​n.307+6046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,020 control chromosomes in the GnomAD database, including 15,460 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 0.33 (15460 hom., cov: 33)
• Consequence: ENSG00000250954 ENST00000505018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 4 publications found

Genes affected

ENSG00000250954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505018.1. 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
	LOC101928622	NR_125902.1		n.307+6046G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250954	ENST00000505018.1	TSL:1	n.307+6046G>A		intron	N/A
	ENSG00000250723	ENST00000505326.6	TSL:4	n.299-14995C>T		intron	N/A
	ENSG00000250723	ENST00000506650.2	TSL:3	n.262-9466C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49631 AN: 151904 Hom.: 15402 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.327 AC: 49749 AN: 152020 Hom.: 15460 Cov.: 33 AF XY: 0.325 AC XY: 24113 AN XY: 74294

African (AFR) AF: 0.818 AC: 33948 AN: 41486

American (AMR) AF: 0.265 AC: 4049 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3464

East Asian (EAS) AF: 0.283 AC: 1458 AN: 5156

South Asian (SAS) AF: 0.164 AC: 789 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1194 AN: 10554

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7102 AN: 67972

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.238 Hom.: 1544

Bravo AF: 0.358

Asia WGS AF: 0.287 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		-0.059

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: rs9306906;

hg19: chr4-33966367;