rs11940562

Variant names:

• chr4-32591327-C-T
• rs11940562
• ENST00000659320.1:n.216-6031G>A

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-6031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,790 control chromosomes in the GnomAD database, including 2,653 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 0.18 (2653 hom., cov: 32)
• Consequence: ENSG00000286784 ENST00000659320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 2 publications found

Genes affected

ENSG00000286784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659320.1. 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
	ENSG00000286784	ENST00000659320.1		n.216-6031G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27845 AN: 151672 Hom.: 2653 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.183 AC: 27850 AN: 151790 Hom.: 2653 Cov.: 32 AF XY: 0.183 AC XY: 13533 AN XY: 74130

African (AFR) AF: 0.172 AC: 7140 AN: 41406

American (AMR) AF: 0.143 AC: 2185 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3464

East Asian (EAS) AF: 0.198 AC: 1009 AN: 5100

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4812

European-Finnish (FIN) AF: 0.145 AC: 1532 AN: 10560

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13447 AN: 67902

Other (OTH) AF: 0.193 AC: 407 AN: 2106

Alfa AF: 0.194 Hom.: 5252

Bravo AF: 0.182

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.45
PhyloP100		-0.77

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: rs11940562;

hg19: chr4-32592949;