11-2172587-C-G

Variant names:

• chr11-2172587-C-G
• rs10840490
• ENST00000729705.1:n.321-1398C>G

Variant summary

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

The ENST00000729705.1(ENSG00000295384):​n.321-1398C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,128 control chromosomes in the GnomAD database, including 2,267 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 (2267 hom., cov: 33)
• Consequence: ENSG00000295384 ENST00000729705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 12 publications found

Genes affected

ENSG00000295384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 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
ENSG00000295384	ENST00000729705.1	n.321-1398C>G		intron_variant	Intron 2 of 2
ENSG00000295384	ENST00000729706.1	n.372-203C>G		intron_variant	Intron 2 of 2
ENSG00000295395	ENST00000729780.1	n.397-162G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25726 AN: 152010 Hom.: 2261 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.169 AC: 25753 AN: 152128 Hom.: 2267 Cov.: 33 AF XY: 0.170 AC XY: 12649 AN XY: 74382

African (AFR) AF: 0.206 AC: 8546 AN: 41472

American (AMR) AF: 0.232 AC: 3545 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.147 AC: 760 AN: 5172

South Asian (SAS) AF: 0.173 AC: 836 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1636 AN: 10608

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9549 AN: 67986

Other (OTH) AF: 0.159 AC: 334 AN: 2106

Alfa AF: 0.0735 Hom.: 81

Bravo AF: 0.175

Asia WGS AF: 0.154 AC: 536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.20
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10840490; hg19: chr11-2193817; COSMIC: COSV60767910;