rs281860601

Positions:

• chr11-5249971-G-A
• chr11-5249971-G-C
• chr11-5249971-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5 BP4

The ENST00000642908.1(ENSG00000284931):​c.316-1484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: 𝑓 0.0000095 (0 hom., cov: 12)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.15

Genes affected

ENSG00000284931 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PP5: Variant 11-5249971-G-A is Pathogenic according to our data. Variant chr11-5249971-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 15035.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5249971G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284931	ENST00000642908.1	c.316-1484C>T		intron_variant				ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.379-1484C>T		intron_variant				ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.00000954 AC: 1 AN: 104850 Hom.: 0 Cov.: 12

Gnomad AFR AF: 0.0000417

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000954 AC: 1 AN: 104850 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 49142

Gnomad4 AFR AF: 0.0000417

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hereditary persistence of fetal hemoglobin Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1991

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281860601; hg19: chr11-5271201;