rs9287724

Positions:

• chr2-10848462-C-A
• chr2-10848462-C-G

Variant summary

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

The ENST00000418835.1(ENSG00000232056):​n.35+851C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,196 control chromosomes in the GnomAD database, including 2,223 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 (2223 hom., cov: 32)
• Consequence: ENSG00000232056 ENST00000418835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000232056 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905973	XR_007086215.1	n.146-192G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232056	ENST00000418835.1	n.35+851C>A		intron_variant		3
LINC01954	ENST00000670239.2	n.272+3957C>A		intron_variant
LINC01954	ENST00000691398.1	n.282+3957C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24429 AN: 152078 Hom.: 2218 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.161 AC: 24453 AN: 152196 Hom.: 2223 Cov.: 32 AF XY: 0.163 AC XY: 12117 AN XY: 74398

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.143

Alfa AF: 0.144 Hom.: 3533

Bravo AF: 0.148

Asia WGS AF: 0.109 AC: 379 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	0.22
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287724; hg19: chr2-10988588;