rs3881751

Variant names:

• chr1-120841859-A-G
• rs3881751
• ENST00000620612.6:c.*1266A>G

Variant summary

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

The ENST00000620612.6(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 ENST00000620612.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

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

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

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

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBPF26	ENST00000620612.6	c.*1266A>G		3_prime_UTR_variant	Exon 36 of 36	5		ENSP00000481542.4
NBPF26	ENST00000652444.2	n.*2218A>G		non_coding_transcript_exon_variant	Exon 21 of 21			ENSP00000498391.2
NBPF26	ENST00000652444.2	n.*2218A>G		3_prime_UTR_variant	Exon 21 of 21			ENSP00000498391.2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 1007 AN: 5430 Hom.: 76 Cov.: 1

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.114 AC: 67 AN: 586

American (AMR) AF: 0.136 AC: 64 AN: 470

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 59 AN: 308

East Asian (EAS) AF: 0.196 AC: 56 AN: 286

South Asian (SAS) AF: 0.121 AC: 34 AN: 280

European-Finnish (FIN) AF: 0.152 AC: 25 AN: 164

Middle Eastern (MID) AF: 0.219 AC: 7 AN: 32

European-Non Finnish (NFE) AF: 0.214 AC: 660 AN: 3078

Other (OTH) AF: 0.185 AC: 17 AN: 92

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3881751; hg19: chr1-148757950;