chr11-38286863-A-G

Position:

• chr11-38286863-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931202.2(LOC105376634):​n.554+38312T>C variant causes a intron, non coding transcript 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: LOC105376634 XR_931202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

LOC105376634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376634	XR_931202.2	n.554+38312T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.0360

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.00913

Gnomad4 FIN AF: 0.00472

Gnomad4 NFE AF: 0.00559

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0228 Hom.: 126

Bravo AF: 0.120

Asia WGS AF: 0.0380 AC: 133 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6484985; hg19: chr11-38308413;