rs11680809

Variant names:

• chr2-112813232-C-A
• rs11680809
• ENST00000762706.1:n.404+42336C>A

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+42336C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,172 control chromosomes in the GnomAD database, including 24,316 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 0.56 (24316 hom., cov: 33)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 9 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
	ENSG00000299339	ENST00000762706.1		n.404+42336C>A		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+42336C>A		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+42336C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84907 AN: 152054 Hom.: 24284 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.558 AC: 84980 AN: 152172 Hom.: 24316 Cov.: 33 AF XY: 0.569 AC XY: 42371 AN XY: 74404

African (AFR) AF: 0.457 AC: 18962 AN: 41482

American (AMR) AF: 0.656 AC: 10040 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1899 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4085 AN: 5186

South Asian (SAS) AF: 0.605 AC: 2919 AN: 4826

European-Finnish (FIN) AF: 0.682 AC: 7226 AN: 10594

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37919 AN: 68000

Other (OTH) AF: 0.573 AC: 1211 AN: 2112

Alfa AF: 0.557 Hom.: 41448

Bravo AF: 0.554

Asia WGS AF: 0.685 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.34
DANN	Benign	0.64
PhyloP100		0.026

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: rs11680809;

hg19: chr2-113570809;

COSMIC: COSV60092714;