rs11692860

Positions:

• chr2-180490796-G-A
• chr2-180490796-G-C
• chr2-180490796-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.0015 (2 hom., cov: 18)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.180490796G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00146 AC: 155 AN: 105822 Hom.: 2 Cov.: 18

Gnomad AFR AF: 0.000135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000910

Gnomad ASJ AF: 0.00108

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00155

Gnomad FIN AF: 0.000244

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00252

Gnomad OTH AF: 0.00143

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

GnomAD4 genome AF: 0.00146 AC: 155 AN: 105864 Hom.: 2 Cov.: 18 AF XY: 0.00147 AC XY: 72 AN XY: 49110

Gnomad4 AFR AF: 0.000135

Gnomad4 AMR AF: 0.000909

Gnomad4 ASJ AF: 0.00108

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00155

Gnomad4 FIN AF: 0.000244

Gnomad4 NFE AF: 0.00252

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000273 Hom.: 89

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11692860; hg19: chr2-181355523;