rs11905013

Variant names:

• chr20-37413237-T-C
• rs11905013
• ENST00000811047.1:n.167+680T>C

Variant summary

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

The ENST00000811047.1(ENSG00000305458):​n.167+680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,950 control chromosomes in the GnomAD database, including 4,809 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 0.21 (4809 hom., cov: 31)
• Consequence: ENSG00000305458 ENST00000811047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 8 publications found

Genes affected

ENSG00000305458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811047.1. 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
	ENSG00000305458	ENST00000811047.1		n.167+680T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31641 AN: 151832 Hom.: 4797 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.209 AC: 31704 AN: 151950 Hom.: 4809 Cov.: 31 AF XY: 0.206 AC XY: 15267 AN XY: 74276

African (AFR) AF: 0.430 AC: 17797 AN: 41358

American (AMR) AF: 0.197 AC: 3006 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1310 AN: 5142

South Asian (SAS) AF: 0.109 AC: 527 AN: 4816

European-Finnish (FIN) AF: 0.0574 AC: 609 AN: 10604

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7464 AN: 67964

Other (OTH) AF: 0.191 AC: 402 AN: 2108

Alfa AF: 0.135 Hom.: 3584

Bravo AF: 0.230

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.81
PhyloP100		0.55

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: rs11905013;

hg19: chr20-36041640;