11-30813663-C-A

Variant names:

• chr11-30813663-C-A
• rs580831
• ENST00000663545.1:n.1153+20335C>A

Variant summary

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

The ENST00000663545.1(ENSG00000287373):​n.1153+20335C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.50 (12216 hom., cov: 12)
• Consequence: ENSG00000287373 ENST00000663545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 2 publications found

Genes affected

ENSG00000287373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663545.1. 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
	ENSG00000287373	ENST00000663545.1		n.1153+20335C>A		intron	N/A
	ENSG00000287373	ENST00000749566.1		n.463+10321C>A		intron	N/A
	ENSG00000287373	ENST00000749567.1		n.1189+20335C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.499 AC: 49948 AN: 100034 Hom.: 12212 Cov.: 12

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.499 AC: 49959 AN: 100062 Hom.: 12216 Cov.: 12 AF XY: 0.494 AC XY: 22955 AN XY: 46438

African (AFR) AF: 0.442 AC: 10252 AN: 23176

American (AMR) AF: 0.525 AC: 4594 AN: 8754

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 1620 AN: 2774

East Asian (EAS) AF: 0.630 AC: 2202 AN: 3498

South Asian (SAS) AF: 0.614 AC: 1448 AN: 2358

European-Finnish (FIN) AF: 0.396 AC: 1756 AN: 4438

Middle Eastern (MID) AF: 0.587 AC: 101 AN: 172

European-Non Finnish (NFE) AF: 0.509 AC: 26971 AN: 52980

Other (OTH) AF: 0.520 AC: 661 AN: 1272

Alfa AF: 0.350 Hom.: 583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.49
DANN	Benign	0.082
PhyloP100		-2.4

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: rs580831;

hg19: chr11-30835210;

COSMIC: COSV67022678;