rs11067763

Positions:

• chr12-115760536-A-G
• chr12-115760536-A-T

Variant summary

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

The ENST00000549163.1(ENSG00000257781):​n.130-4918A>G 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 0.169 in 152,154 control chromosomes in the GnomAD database, including 2,840 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 0.17 (2840 hom., cov: 32)
• Consequence: ENST00000549163.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370003	XR_945389.3	n.118+2412T>C		intron_variant, non_coding_transcript_variant
LOC105370003	XR_945388.3	n.118+2412T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000549163.1	n.130-4918A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25638 AN: 152036 Hom.: 2827 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.169 AC: 25678 AN: 152154 Hom.: 2840 Cov.: 32 AF XY: 0.172 AC XY: 12761 AN XY: 74396

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.187

Alfa AF: 0.145 Hom.: 328

Bravo AF: 0.179

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11067763; hg19: chr12-116198341;