rs10931468

Variant names:

• chr2-190673836-C-A
• rs10931468
• NM_005966.4:c.1005+684C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-190673836-C-A
• chr2-190673836-C-G
• chr2-190673836-C-T

Variant summary

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

The NM_005966.4(NAB1):​c.1005+684C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,072 control chromosomes in the GnomAD database, including 2,887 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 0.18 (2887 hom., cov: 32)
• Consequence: NAB1 NM_005966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 37 publications found

Genes affected

NAB1 (HGNC:7626): (NGFI-A binding protein 1) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to act upstream of or within endochondral ossification; nervous system development; and regulation of epidermis development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAB1	NM_005966.4	c.1005+684C>A		intron_variant	Intron 6 of 9	ENST00000337386.10	NP_005957.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAB1	ENST00000337386.10	c.1005+684C>A		intron_variant	Intron 6 of 9	1	NM_005966.4	ENSP00000336894.5

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27617 AN: 151954 Hom.: 2877 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.182 AC: 27651 AN: 152072 Hom.: 2887 Cov.: 32 AF XY: 0.186 AC XY: 13829 AN XY: 74330

African (AFR) AF: 0.228 AC: 9473 AN: 41468

American (AMR) AF: 0.258 AC: 3936 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 343 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2078 AN: 5164

South Asian (SAS) AF: 0.206 AC: 996 AN: 4824

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9054 AN: 67980

Other (OTH) AF: 0.173 AC: 364 AN: 2106

Alfa AF: 0.152 Hom.: 9310

Bravo AF: 0.195

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.64
PhyloP100		-0.23
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: rs10931468; hg19: chr2-191538562;