rs13387833

Positions:

• chr2-75201270-G-A

Variant summary

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

The NR_168009.1(LOC105374811):​n.372+44955G>A 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 0.068 (357 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: LOC105374811 NR_168009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

Genes affected

LOC105374811 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374811	NR_168009.1	n.372+44955G>A		intron_variant, non_coding_transcript_variant
LOC105374811	NR_168010.1	n.366+44955G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 8930 AN: 131718 Hom.: 358 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.0251

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0373

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.0880

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0699

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: AS_VQSR AF: 0.0678 AC: 8933 AN: 131842 Hom.: 357 Cov.: 20 AF XY: 0.0662 AC XY: 4186 AN XY: 63234

Gnomad4 AFR AF: 0.0572

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0373

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0647

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.0703

Alfa AF: 0.0671 Hom.: 54

Bravo AF: 0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13387833; hg19: chr2-75428396;