rs11168351

Positions:

• chr12-48009982-G-A

Variant summary

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

The ENST00000552958.5(ENSG00000258203):​n.36+1210C>T 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 0.275 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: ENST00000552958.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000552958.5	n.36+1210C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000546804.1	n.180+445C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.286

Alfa AF: 0.356 Hom.: 9434

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11168351; hg19: chr12-48403765;