chr2-13628292-T-G

Variant names:

• chr2-13628292-T-G
• rs1510823
• NR_188380.1:n.206+19131T>G

Variant summary

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

The NR_188380.1(LOC105373438):​n.206+19131T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 151,898 control chromosomes in the GnomAD database, including 48,999 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 0.79 (48999 hom., cov: 31)
• Consequence: LOC105373438 NR_188380.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 2 publications found

Genes affected

LOC105373438 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373438	NR_188380.1	n.206+19131T>G		intron_variant	Intron 2 of 4
LOC105373438	NR_188381.1	n.206+19131T>G		intron_variant	Intron 2 of 2
LOC105373438	NR_188382.1	n.206+19131T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120149 AN: 151778 Hom.: 48992 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.791 AC: 120212 AN: 151898 Hom.: 48999 Cov.: 31 AF XY: 0.784 AC XY: 58228 AN XY: 74252

African (AFR) AF: 0.643 AC: 26638 AN: 41412

American (AMR) AF: 0.755 AC: 11477 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3068 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2059 AN: 5150

South Asian (SAS) AF: 0.745 AC: 3586 AN: 4814

European-Finnish (FIN) AF: 0.839 AC: 8878 AN: 10578

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61689 AN: 67956

Other (OTH) AF: 0.806 AC: 1699 AN: 2108

Alfa AF: 0.836 Hom.: 7002

Bravo AF: 0.777

Asia WGS AF: 0.625 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.76
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs1510823; hg19: chr2-13768417;