rs11685593

Variant names:

• chr2-127130545-C-T
• rs11685593
• ENST00000726607.1:n.342-4715C>T

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-4715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,854 control chromosomes in the GnomAD database, including 1,724 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 0.14 (1724 hom., cov: 31)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 13 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373605	XR_923310.3	n.449-2693C>T		intron_variant	Intron 2 of 3
LOC105373605	XR_923311.4	n.846-2693C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294899	ENST00000726607.1	n.342-4715C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21039 AN: 151736 Hom.: 1718 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.139 AC: 21057 AN: 151854 Hom.: 1724 Cov.: 31 AF XY: 0.137 AC XY: 10168 AN XY: 74208

African (AFR) AF: 0.0602 AC: 2493 AN: 41396

American (AMR) AF: 0.149 AC: 2269 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3472

East Asian (EAS) AF: 0.100 AC: 520 AN: 5176

South Asian (SAS) AF: 0.0646 AC: 311 AN: 4814

European-Finnish (FIN) AF: 0.176 AC: 1854 AN: 10512

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12323 AN: 67926

Other (OTH) AF: 0.142 AC: 300 AN: 2108

Alfa AF: 0.150 Hom.: 1479

Bravo AF: 0.135

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs11685593; hg19: chr2-127888121;