11-38286863-A-G

Variant names:

• chr11-38286863-A-G
• rs6484985
• ENST00000822141.1:n.450+38312T>C

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.450+38312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,744 control chromosomes in the GnomAD database, including 2,738 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 0.11 (2738 hom., cov: 32)
• Consequence: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• 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 (AFR) allele frequency at 95% confidence interval = 0.348 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+38312T>C		intron	N/A
	ENSG00000306949	ENST00000822142.1		n.454+38312T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15927 AN: 151626 Hom.: 2725 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00559

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.105 AC: 15978 AN: 151744 Hom.: 2738 Cov.: 32 AF XY: 0.102 AC XY: 7562 AN XY: 74178

African (AFR) AF: 0.353 AC: 14617 AN: 41398

American (AMR) AF: 0.0360 AC: 548 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3466

East Asian (EAS) AF: 0.0265 AC: 137 AN: 5174

South Asian (SAS) AF: 0.00913 AC: 44 AN: 4818

European-Finnish (FIN) AF: 0.00472 AC: 50 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00559 AC: 379 AN: 67762

Other (OTH) AF: 0.0769 AC: 162 AN: 2106

Alfa AF: 0.0273 Hom.: 203

Bravo AF: 0.120

Asia WGS AF: 0.0380 AC: 133 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.40

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: rs6484985;

hg19: chr11-38308413;