rs9266406

Variant names:

• chr6-31368641-G-A
• rs9266406
• ENST00000649421.2:n.274+1311G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31368641-G-A
• chr6-31368641-G-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+1311G>A 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 152,044 control chromosomes in the GnomAD database, including 3,825 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 (3825 hom., cov: 31)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285647	ENST00000649421.2	n.274+1311G>A		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-13339G>A		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-6242G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33316 AN: 151926 Hom.: 3825 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.203

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: 33330 AN: 152044 Hom.: 3825 Cov.: 31 AF XY: 0.225 AC XY: 16740 AN XY: 74320

African (AFR) AF: 0.229 AC: 9507 AN: 41462

American (AMR) AF: 0.202 AC: 3085 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1936 AN: 5154

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10556

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

European-Non Finnish (NFE) AF: 0.199 AC: 13519 AN: 67972

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.210 Hom.: 6618

Bravo AF: 0.218

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.68
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9266406; hg19: chr6-31336418;