NR_187774.1:n.1299A>G

Variant names:

• chr19-9720508-A-G
• rs2112837
• NR_187774.1:n.1299A>G

Variant summary

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

The NR_187774.1(LOC105372270):​n.1299A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,110 control chromosomes in the GnomAD database, including 6,433 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 0.27 (6433 hom., cov: 32)
• Consequence: LOC105372270 NR_187774.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 4 publications found

Genes affected

LOC105372270 (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 (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372270	NR_187774.1	n.1299A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291231	ENST00000779066.1	n.136+15235T>C		intron_variant	Intron 1 of 3
ENSG00000291231	ENST00000779067.1	n.169+15235T>C		intron_variant	Intron 1 of 3
ENSG00000291231	ENST00000779068.1	n.167+15235T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40853 AN: 151990 Hom.: 6406 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.269 AC: 40940 AN: 152110 Hom.: 6433 Cov.: 32 AF XY: 0.272 AC XY: 20221 AN XY: 74392

African (AFR) AF: 0.412 AC: 17069 AN: 41448

American (AMR) AF: 0.345 AC: 5274 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.0648 AC: 336 AN: 5182

South Asian (SAS) AF: 0.206 AC: 993 AN: 4828

European-Finnish (FIN) AF: 0.248 AC: 2625 AN: 10592

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13439 AN: 67990

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.167 Hom.: 525

Bravo AF: 0.282

Asia WGS AF: 0.202 AC: 705 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	3.1
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2112837; hg19: chr19-9831184;