rs11692045

Variant names:

• chr2-41723813-A-G
• rs11692045
• ENST00000660664.1:n.110-874A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660664.1(ENSG00000287145):​n.110-874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,070 control chromosomes in the GnomAD database, including 6,679 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 0.28 (6679 hom., cov: 32)
• Consequence: ENSG00000287145 ENST00000660664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 6 publications found

Genes affected

ENSG00000287145 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287145	ENST00000660664.1	n.110-874A>G		intron_variant	Intron 1 of 2
ENSG00000304630	ENST00000805042.1	n.132-11226T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42992 AN: 151952 Hom.: 6669 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.283 AC: 43033 AN: 152070 Hom.: 6679 Cov.: 32 AF XY: 0.281 AC XY: 20852 AN XY: 74338

African (AFR) AF: 0.392 AC: 16247 AN: 41464

American (AMR) AF: 0.197 AC: 3006 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3470

East Asian (EAS) AF: 0.122 AC: 630 AN: 5176

South Asian (SAS) AF: 0.203 AC: 976 AN: 4812

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10566

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17396 AN: 67982

Other (OTH) AF: 0.219 AC: 463 AN: 2110

Alfa AF: 0.292 Hom.: 1311

Bravo AF: 0.277

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.8
DANN	Benign	0.56
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs11692045; hg19: chr2-41950953;