rs11903757

chr2-191722478-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088698.1(LOC124908062):n.365-10898T>C variant causes a intron, non coding transcript 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: LOC124908062 XR_007088698.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

LOC124908062 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124908062	XR_007088698.1	n.365-10898T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NABP1	ENST00000674262.1	c.*7815+12695T>C		intron_variant, NMD_transcript_variant
NABP1	ENST00000674360.1	c.*7649-13438T>C		intron_variant, NMD_transcript_variant
NABP1	ENST00000674406.1	c.*7815+12695T>C		intron_variant, NMD_transcript_variant
NABP1	ENST00000674414.1	c.*7649-13438T>C		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0578

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.144

Alfa AF: 0.157 Hom.: 480

Bravo AF: 0.148

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.48
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11903757; hg19: chr2-192587204;