rs10858946

Positions:

• chr12-90050265-A-C

Variant summary

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

The ENST00000651272.1(ENSG00000258216):​n.571-44171A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,102 control chromosomes in the GnomAD database, including 4,246 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 0.21 (4246 hom., cov: 31)
• Consequence: ENST00000651272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369890	XR_001749246.2	n.1019-16731A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651272.1	n.571-44171A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32119 AN: 151984 Hom.: 4244 Cov.: 31

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.211 AC: 32125 AN: 152102 Hom.: 4246 Cov.: 31 AF XY: 0.209 AC XY: 15569 AN XY: 74350

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.212

Alfa AF: 0.247 Hom.: 644

Bravo AF: 0.193

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858946; hg19: chr12-90444042;