chr1-120841859-A-G

Position:

• chr1-120841859-A-G

Variant summary

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

The NM_001405520.1(NBPF26):​c.*1266A>G variant causes a 3 prime UTR 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 0.18 (76 hom., cov: 1)
  • Failed GnomAD Quality Control
• Consequence: NBPF26 NM_001405520.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

NBPF26 (HGNC:49571): (NBPF member 26) Predicted to enable calcium ion binding activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBPF26	NM_001405520.1	c.*1266A>G		3_prime_UTR_variant	36/36		NP_001392449.1
NBPF26	NM_001351372.2	c.*1266A>G		3_prime_UTR_variant	34/34		NP_001338301.2
NBPF26	NM_001395637.2	c.*1266A>G		3_prime_UTR_variant	30/30		NP_001382566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBPF26	ENST00000620612.6	c.*1266A>G		3_prime_UTR_variant	36/36	5		ENSP00000481542	P1
NBPF26	ENST00000652444.2	c.*2218A>G		3_prime_UTR_variant, NMD_transcript_variant	21/21			ENSP00000498391

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1007 AN: 5430 Hom.: 76 Cov.: 1 FAILED QC

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.211

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.190

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: 0.185 AC: 1006 AN: 5446 Hom.: 76 Cov.: 1 AF XY: 0.180 AC XY: 441 AN XY: 2450

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.185

Alfa AF: 0.764 Hom.: 3871

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3881751; hg19: chr1-148757950;