rs72934505

Variant names:

• chr2-203051764-T-G
• rs72934505
• NM_001378026.1:c.305+1789T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378026.1(NBEAL1):​c.305+1789T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 152,214 control chromosomes in the GnomAD database, including 765 homozygotes. 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 0.092 (765 hom., cov: 31)
• Consequence: NBEAL1 NM_001378026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 23 publications found

Genes affected

NBEAL1 (HGNC:20681): (neurobeachin like 1) Predicted to enable protein kinase binding activity. Predicted to be involved in protein localization. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBEAL1	NM_001378026.1	c.305+1789T>G		intron_variant	Intron 4 of 55	ENST00000683969.1	NP_001364955.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NBEAL1	ENST00000683969.1	c.305+1789T>G		intron_variant	Intron 4 of 55		NM_001378026.1	ENSP00000508055.1

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14006 AN: 152096 Hom.: 760 Cov.: 31

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0921 AC: 14020 AN: 152214 Hom.: 765 Cov.: 31 AF XY: 0.0892 AC XY: 6641 AN XY: 74420

African (AFR) AF: 0.0432 AC: 1796 AN: 41546

American (AMR) AF: 0.0973 AC: 1486 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3468

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5184

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4826

European-Finnish (FIN) AF: 0.106 AC: 1127 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8497 AN: 68008

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.110 Hom.: 122

Bravo AF: 0.0909

Asia WGS AF: 0.0410 AC: 143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs72934505; hg19: chr2-203916487;