11-38255470-C-T

Variant names:

• chr11-38255470-C-T
• rs9300027
• ENST00000822141.1:n.451-54422G>A

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.451-54422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,006 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: -0.933
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822141.1. 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
	ENSG00000306949	ENST00000822141.1		n.451-54422G>A		intron	N/A
	ENSG00000306949	ENST00000822142.1		n.455-54422G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13096 AN: 151888 Hom.: 1820 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00563

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0865 AC: 13142 AN: 152006 Hom.: 1830 Cov.: 32 AF XY: 0.0833 AC XY: 6192 AN XY: 74342

African (AFR) AF: 0.287 AC: 11893 AN: 41458

American (AMR) AF: 0.0314 AC: 479 AN: 15266

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

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5176

South Asian (SAS) AF: 0.00829 AC: 40 AN: 4828

European-Finnish (FIN) AF: 0.00472 AC: 50 AN: 10604

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

European-Non Finnish (NFE) AF: 0.00563 AC: 382 AN: 67884

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0649 Hom.: 195

Bravo AF: 0.0974

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.64
PhyloP100		-0.93

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: rs9300027;

hg19: chr11-38277020;