chr11-38257400-T-A

Position:

• chr11-38257400-T-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_931202.2(LOC105376634):​n.555-56352A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.48 (405 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LOC105376634 XR_931202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

LOC105376634 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376634	XR_931202.2	n.555-56352A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 8494 AN: 17698 Hom.: 405 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.505

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.480 AC: 8511 AN: 17742 Hom.: 405 Cov.: 0 AF XY: 0.481 AC XY: 4348 AN XY: 9042

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.505

Alfa AF: 0.523 Hom.: 333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5004866; hg19: chr11-38278950;