rs11696364

Variant names:

• chr20-1031383-C-A
• rs11696364
• ENST00000778971.1:n.315G>T

Variant summary

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

The ENST00000664648.2(ENSG00000286787):​n.352+1G>T variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,202 control chromosomes in the GnomAD database, including 315 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 0.054 (315 hom., cov: 32)
• Consequence: ENSG00000286787 ENST00000664648.2 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 5 publications found

Genes affected

ENSG00000286787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664648.2. 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
	ENSG00000286787	ENST00000778971.1		n.315G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286787	ENST00000664648.2		n.352+1G>T		splice_donor intron	N/A
	ENSG00000301438	ENST00000778881.1		n.216+18979C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8194 AN: 152084 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0538 AC: 8190 AN: 152202 Hom.: 315 Cov.: 32 AF XY: 0.0520 AC XY: 3870 AN XY: 74424

African (AFR) AF: 0.0154 AC: 638 AN: 41538

American (AMR) AF: 0.0390 AC: 596 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4828

European-Finnish (FIN) AF: 0.0885 AC: 937 AN: 10588

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5682 AN: 68006

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0649 Hom.: 824

Bravo AF: 0.0492

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		0.026

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11696364; hg19: chr20-1012026;