rs11105468

Positions:

• chr12-89935056-T-A

Variant summary

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

The ENST00000651272.1(ENSG00000258216):​n.504+13887T>A 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 0.251 in 152,020 control chromosomes in the GnomAD database, including 4,912 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 0.25 (4912 hom., cov: 32)
• Consequence: ENST00000651272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369890	XR_001749246.2	n.649-766T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651272.1	n.504+13887T>A		intron_variant, non_coding_transcript_variant
	ENST00000547370.5	n.331-766T>A		intron_variant, non_coding_transcript_variant		4
	ENST00000549551.1	n.172+13887T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38174 AN: 151902 Hom.: 4905 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.251 AC: 38193 AN: 152020 Hom.: 4912 Cov.: 32 AF XY: 0.246 AC XY: 18287 AN XY: 74296

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.241

Alfa AF: 0.263 Hom.: 664

Bravo AF: 0.241

Asia WGS AF: 0.135 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11105468; hg19: chr12-90328833;