rs11694463

Positions:

• chr2-12641495-T-C

Variant summary

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

The variant allele was found at a frequency of 0.112 in 152,264 control chromosomes in the GnomAD database, including 979 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 0.11 (979 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12641495T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000664018.1	n.579-32734T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17066 AN: 152146 Hom.: 979 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0933

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.112 AC: 17074 AN: 152264 Hom.: 979 Cov.: 33 AF XY: 0.112 AC XY: 8325 AN XY: 74452

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.0933

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.127

Alfa AF: 0.109 Hom.: 544

Bravo AF: 0.113

Asia WGS AF: 0.129 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11694463; hg19: chr2-12781621;