rs12376718

Variant names:

• chr9-29531581-C-A
• rs12376718
• ENST00000850880.1:n.99-21186C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-29531581-C-A
• chr9-29531581-C-T

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.99-21186C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,990 control chromosomes in the GnomAD database, including 4,616 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 0.24 (4616 hom., cov: 32)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 2 publications found

Genes affected

ENSG00000300941 (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 = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300941	ENST00000850880.1	n.99-21186C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36063 AN: 151872 Hom.: 4617 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.237 AC: 36068 AN: 151990 Hom.: 4616 Cov.: 32 AF XY: 0.239 AC XY: 17741 AN XY: 74278

African (AFR) AF: 0.159 AC: 6602 AN: 41446

American (AMR) AF: 0.278 AC: 4251 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3468

East Asian (EAS) AF: 0.0876 AC: 453 AN: 5174

South Asian (SAS) AF: 0.165 AC: 794 AN: 4824

European-Finnish (FIN) AF: 0.299 AC: 3151 AN: 10542

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19188 AN: 67964

Other (OTH) AF: 0.236 AC: 497 AN: 2104

Alfa AF: 0.245 Hom.: 2469

Bravo AF: 0.234

Asia WGS AF: 0.151 AC: 523 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	0.36
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs12376718; hg19: chr9-29531579;