rs10506943

Variant names:

• chr12-87720599-T-C
• rs10506943
• ENST00000841431.1:n.133-5972A>G

Variant summary

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

The ENST00000841431.1(ENSG00000293096):​n.133-5972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0375 in 152,240 control chromosomes in the GnomAD database, including 154 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 0.037 (154 hom., cov: 32)
• Consequence: ENSG00000293096 ENST00000841431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 2 publications found

Genes affected

ENSG00000293096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0702 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
ENSG00000293096	ENST00000841431.1	n.133-5972A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0374 AC: 5691 AN: 152122 Hom.: 151 Cov.: 32

Gnomad AFR AF: 0.00810

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0375 AC: 5703 AN: 152240 Hom.: 154 Cov.: 32 AF XY: 0.0383 AC XY: 2849 AN XY: 74398

African (AFR) AF: 0.00808 AC: 336 AN: 41578

American (AMR) AF: 0.0738 AC: 1126 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3472

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4828

European-Finnish (FIN) AF: 0.0567 AC: 602 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0448 AC: 3044 AN: 67988

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.0415 Hom.: 19

Bravo AF: 0.0383

Asia WGS AF: 0.0230 AC: 81 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10506943; hg19: chr12-88114376;