rs11168351

Variant names:

• chr12-48009982-G-A
• rs11168351
• ENST00000546804.1:n.180+445C>T

Variant summary

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

The ENST00000546804.1(ENSG00000258203):​n.180+445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,102 control chromosomes in the GnomAD database, including 7,019 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 0.27 (7019 hom., cov: 33)
• Consequence: ENSG00000258203 ENST00000546804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 10 publications found

Genes affected

ENSG00000258203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000258203	ENST00000546804.1	n.180+445C>T		intron_variant	Intron 2 of 4	4
ENSG00000258203	ENST00000552958.5	n.36+1210C>T		intron_variant	Intron 1 of 3	4
ENSG00000258203	ENST00000833577.1	n.178-457C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41797 AN: 151984 Hom.: 7019 Cov.: 33

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.275 AC: 41806 AN: 152102 Hom.: 7019 Cov.: 33 AF XY: 0.275 AC XY: 20468 AN XY: 74330

African (AFR) AF: 0.0784 AC: 3254 AN: 41524

American (AMR) AF: 0.296 AC: 4516 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.116 AC: 599 AN: 5174

South Asian (SAS) AF: 0.393 AC: 1897 AN: 4822

European-Finnish (FIN) AF: 0.339 AC: 3574 AN: 10550

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25587 AN: 67982

Other (OTH) AF: 0.286 AC: 603 AN: 2112

Alfa AF: 0.320 Hom.: 12998

Bravo AF: 0.259

Asia WGS AF: 0.240 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11168351; hg19: chr12-48403765;