rs10859418

Variant names:

• chr12-93053544-G-A
• rs10859418
• ENST00000549930.1:n.99-48946C>T

Variant summary

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

The ENST00000549930.1(ENSG00000257252):​n.99-48946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 151,552 control chromosomes in the GnomAD database, including 297 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 0.050 (297 hom., cov: 32)
• Consequence: ENSG00000257252 ENST00000549930.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 1 publications found

Genes affected

ENSG00000257252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643339	NR_040096.1	n.428-48946C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257252	ENST00000549930.1	n.99-48946C>T		intron_variant	Intron 1 of 2	5
ENSG00000257252	ENST00000550324.7	n.169-48946C>T		intron_variant	Intron 1 of 2	3
ENSG00000257252	ENST00000754393.1	n.767-48946C>T		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7503 AN: 151444 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.0632

Gnomad MID AF: 0.0129

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0379

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

GnomAD4 genome AF: 0.0496 AC: 7517 AN: 151552 Hom.: 297 Cov.: 32 AF XY: 0.0518 AC XY: 3836 AN XY: 74054

African (AFR) AF: 0.103 AC: 4248 AN: 41410

American (AMR) AF: 0.0203 AC: 308 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3468

East Asian (EAS) AF: 0.103 AC: 532 AN: 5162

South Asian (SAS) AF: 0.0762 AC: 367 AN: 4814

European-Finnish (FIN) AF: 0.0632 AC: 650 AN: 10288

Middle Eastern (MID) AF: 0.0139 AC: 4 AN: 288

European-Non Finnish (NFE) AF: 0.0185 AC: 1257 AN: 67896

Other (OTH) AF: 0.0389 AC: 82 AN: 2106

Alfa AF: 0.0421 Hom.: 38

Bravo AF: 0.0474

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.32
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10859418; hg19: chr12-93447320;