rs2796146

chr1-234792214-G-Achr1-234792214-G-T

Variant summary

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

The XR_007066954.1(LOC124904557):n.669+1518C>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 0.34 (2 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: LOC124904557 XR_007066954.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

Genes affected

LOC124904557 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904557	XR_007066954.1	n.669+1518C>T		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: 33263 AN: 98352 Hom.: 2 Cov.: 37 FAILED QC

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.384

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.340

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: 0.338 AC: 33274 AN: 98448 Hom.: 2 Cov.: 37 AF XY: 0.333 AC XY: 15915 AN XY: 47792

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.341

Alfa AF: 0.258 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2796146; hg19: chr1-234927961;