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 ENST00000540356.1(ENSG00000260877):​n.124-8193C>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 ENST00000540356.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369370	XR_950269.4	n.467-8193C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260877	ENST00000540356.1	n.124-8193C>A		intron_variant	Intron 1 of 3	3
ENSG00000260877	ENST00000541137.5	n.247-8193C>A		intron_variant	Intron 2 of 4	3
ENSG00000260877	ENST00000544781.5	n.325-8193C>A		intron_variant	Intron 2 of 2	2
ENSG00000260877	ENST00000561588.3	n.170-12853C>A		intron_variant	Intron 1 of 2	3

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 v4.3

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

Other links and lift over

dbSNP: rs11600497; hg19: chr11-69173318;