rs11903757

Variant names:

• chr2-191722478-T-C
• rs11903757
• ENST00000674262.1:n.*7815+12695T>C

Variant summary

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

The ENST00000674262.1(NABP1):​n.*7815+12695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,074 control chromosomes in the GnomAD database, including 2,052 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 0.16 (2052 hom., cov: 32)
• Consequence: NABP1 ENST00000674262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 52 publications found

Genes affected

NABP1 (HGNC:26232): (nucleic acid binding protein 1) Single-stranded DNA (ssDNA)-binding proteins, such as OBFC2A, are ubiquitous and essential for a variety of DNA metabolic processes, including replication, recombination, and detection and repair of damage (Richard et al., 2008 [PubMed 18449195]).[supplied by OMIM, Jun 2008]

LOC124908062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674262.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NABP1	ENST00000674262.1		n.*7815+12695T>C		intron	N/A	ENSP00000501487.1	Q96AH0-1
	NABP1	ENST00000674360.1		n.*7649-13438T>C		intron	N/A	ENSP00000501480.1	Q96AH0-2
	NABP1	ENST00000674406.1		n.*7815+12695T>C		intron	N/A	ENSP00000501496.1	Q96AH0-2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23852 AN: 151956 Hom.: 2050 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.157 AC: 23871 AN: 152074 Hom.: 2052 Cov.: 32 AF XY: 0.160 AC XY: 11927 AN XY: 74330

African (AFR) AF: 0.148 AC: 6145 AN: 41488

American (AMR) AF: 0.156 AC: 2380 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3460

East Asian (EAS) AF: 0.0578 AC: 299 AN: 5176

South Asian (SAS) AF: 0.0946 AC: 456 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10548

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10712 AN: 67980

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.153 Hom.: 3189

Bravo AF: 0.148

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.40
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11903757;

hg19: chr2-192587204;