11-38263951-T-C

Variant names:

• chr11-38263951-T-C
• rs10836945
• ENST00000822141.1:n.450+61224A>G

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.450+61224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 151,970 control chromosomes in the GnomAD database, including 51,407 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 0.79 (51407 hom., cov: 32)
• Consequence: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 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.450+61224A>G		intron	N/A
	ENSG00000306949	ENST00000822142.1		n.454+61224A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119373 AN: 151852 Hom.: 51403 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.786 AC: 119402 AN: 151970 Hom.: 51407 Cov.: 32 AF XY: 0.787 AC XY: 58432 AN XY: 74260

African (AFR) AF: 0.401 AC: 16578 AN: 41384

American (AMR) AF: 0.892 AC: 13625 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3333 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4067 AN: 5156

South Asian (SAS) AF: 0.801 AC: 3856 AN: 4816

European-Finnish (FIN) AF: 0.938 AC: 9889 AN: 10546

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65131 AN: 67998

Other (OTH) AF: 0.835 AC: 1763 AN: 2112

Alfa AF: 0.903 Hom.: 177722

Bravo AF: 0.767

Asia WGS AF: 0.782 AC: 2721 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.61
PhyloP100		0.27

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: rs10836945;

hg19: chr11-38285501;