rs5004866

Variant names:

• chr11-38257400-T-A
• rs5004866
• ENST00000822141.1:n.451-56352A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-38257400-T-A
• chr11-38257400-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000822141.1(ENSG00000306949):​n.451-56352A>T variant causes a intron 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: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 1 publications found

Genes affected

ENSG00000306949 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306949	ENST00000822141.1		n.451-56352A>T		intron	N/A
	ENSG00000306949	ENST00000822142.1		n.455-56352A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 8494 AN: 17698 Hom.: 405 Cov.: 0

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

African (AFR) AF: 0.468 AC: 4306 AN: 9198

American (AMR) AF: 0.480 AC: 543 AN: 1132

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 74 AN: 170

East Asian (EAS) AF: 0.550 AC: 783 AN: 1424

South Asian (SAS) AF: 0.522 AC: 531 AN: 1018

European-Finnish (FIN) AF: 0.496 AC: 521 AN: 1050

Middle Eastern (MID) AF: 0.500 AC: 8 AN: 16

European-Non Finnish (NFE) AF: 0.466 AC: 1640 AN: 3522

Other (OTH) AF: 0.505 AC: 105 AN: 208

Alfa AF: 0.523 Hom.: 333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs5004866; hg19: chr11-38278950;