rs11680911

Variant names:

• chr2-127131181-A-C
• rs11680911
• ENST00000726607.1:n.342-4079A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-127131181-A-C
• chr2-127131181-A-T

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-4079A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,174 control chromosomes in the GnomAD database, including 6,164 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 (6164 hom., cov: 32)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 14 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294899	ENST00000726607.1		n.342-4079A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41887 AN: 152056 Hom.: 6156 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 41941 AN: 152174 Hom.: 6164 Cov.: 32 AF XY: 0.271 AC XY: 20145 AN XY: 74406

African (AFR) AF: 0.209 AC: 8670 AN: 41490

American (AMR) AF: 0.252 AC: 3854 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3468

East Asian (EAS) AF: 0.111 AC: 576 AN: 5190

South Asian (SAS) AF: 0.139 AC: 670 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3365 AN: 10592

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22716 AN: 67982

Other (OTH) AF: 0.273 AC: 577 AN: 2114

Alfa AF: 0.145 Hom.: 325

Bravo AF: 0.269

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.36
PhyloP100		-0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11680911;

hg19: chr2-127888757;