rs9787877

Variant names:

• chr11-69229042-T-C
• rs9787877
• NR_188530.1:n.3148A>G

Variant summary

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

The NR_188530.1(LOC105369367):​n.3148A>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 0.529 in 149,968 control chromosomes in the GnomAD database, including 22,207 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 0.53 (22207 hom., cov: 30)
• Consequence: LOC105369367 NR_188530.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 12 publications found

Genes affected

LOC105369367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369367	NR_188530.1	n.3148A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105369367	NR_188531.1	n.2482A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301530	ENST00000779509.1	n.139-19319T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 79215 AN: 149844 Hom.: 22170 Cov.: 30

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.529 AC: 79305 AN: 149968 Hom.: 22207 Cov.: 30 AF XY: 0.521 AC XY: 38125 AN XY: 73162

African (AFR) AF: 0.695 AC: 28193 AN: 40578

American (AMR) AF: 0.398 AC: 5983 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2282 AN: 3456

East Asian (EAS) AF: 0.0745 AC: 352 AN: 4722

South Asian (SAS) AF: 0.344 AC: 1572 AN: 4568

European-Finnish (FIN) AF: 0.468 AC: 4909 AN: 10486

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34319 AN: 67818

Other (OTH) AF: 0.539 AC: 1126 AN: 2090

Alfa AF: 0.494 Hom.: 14389

Bravo AF: 0.527

Asia WGS AF: 0.298 AC: 1037 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	1.6
DANN	Benign	0.30
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9787877; hg19: chr11-68996509;