rs11600497

Variant names:

• chr11-69358550-C-A
• rs11600497
• ENST00000540356.1:n.124-8193C>A

Variant summary

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

The ENST00000544781.5(ENSG00000260877):​n.325-8193C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,168 control chromosomes in the GnomAD database, including 3,003 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 0.19 (3003 hom., cov: 33)
• Consequence: ENSG00000260877 ENST00000544781.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 3 publications found

Genes affected

ENSG00000260877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000544781.5. 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
	ENSG00000260877	ENST00000540356.1	TSL:3	n.124-8193C>A		intron	N/A
	ENSG00000260877	ENST00000541137.5	TSL:3	n.247-8193C>A		intron	N/A
	ENSG00000260877	ENST00000544781.5	TSL:2	n.325-8193C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28635 AN: 152050 Hom.: 2999 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.188 AC: 28682 AN: 152168 Hom.: 3003 Cov.: 33 AF XY: 0.186 AC XY: 13830 AN XY: 74396

African (AFR) AF: 0.250 AC: 10387 AN: 41504

American (AMR) AF: 0.263 AC: 4025 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1698 AN: 5156

South Asian (SAS) AF: 0.117 AC: 566 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9636 AN: 67984

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.156 Hom.: 3529

Bravo AF: 0.205

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		-0.50

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: rs11600497;

hg19: chr11-69173318;