rs9266399

Variant names:

• chr6-31368029-A-T
• rs9266399
• ENST00000649421.2:n.274+699A>T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+699A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,974 control chromosomes in the GnomAD database, including 3,820 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 0.22 (3820 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 13 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649421.2. 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
	ENSG00000285647	ENST00000649421.2		n.274+699A>T		intron	N/A
	ENSG00000298426	ENST00000755446.1		n.326+13832A>T		intron	N/A
	ENSG00000285647	ENST00000755530.1		n.203-6854A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33320 AN: 151856 Hom.: 3820 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.219 AC: 33334 AN: 151974 Hom.: 3820 Cov.: 32 AF XY: 0.225 AC XY: 16733 AN XY: 74250

African (AFR) AF: 0.229 AC: 9503 AN: 41414

American (AMR) AF: 0.201 AC: 3079 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 727 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1950 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1641 AN: 4822

European-Finnish (FIN) AF: 0.204 AC: 2150 AN: 10544

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67952

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.207 Hom.: 1905

Bravo AF: 0.218

Asia WGS AF: 0.303 AC: 1054 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.3
DANN	Benign	0.79
PhyloP100		0.65

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: rs9266399;

hg19: chr6-31335806;