rs9300026

Variant names:

• chr11-38254955-T-C
• rs9300026
• ENST00000822141.1:n.451-53907A>G

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.451-53907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 152,066 control chromosomes in the GnomAD database, including 1,830 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 0.086 (1830 hom., cov: 32)
• Consequence: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 0 publications found

Genes affected

ENSG00000306949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376634	XR_931202.2	n.555-53907A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306949	ENST00000822141.1	n.451-53907A>G		intron_variant	Intron 2 of 3
ENSG00000306949	ENST00000822142.1	n.455-53907A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13086 AN: 151948 Hom.: 1820 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.00788

Gnomad FIN AF: 0.00471

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00561

Gnomad OTH AF: 0.0655

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

GnomAD4 genome AF: 0.0864 AC: 13132 AN: 152066 Hom.: 1830 Cov.: 32 AF XY: 0.0831 AC XY: 6178 AN XY: 74346

African (AFR) AF: 0.287 AC: 11886 AN: 41438

American (AMR) AF: 0.0313 AC: 478 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3472

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5180

South Asian (SAS) AF: 0.00830 AC: 40 AN: 4820

European-Finnish (FIN) AF: 0.00471 AC: 50 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00561 AC: 381 AN: 67954

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0702 Hom.: 245

Bravo AF: 0.0974

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs9300026; hg19: chr11-38276505;