11-81785217-C-A

Variant names:

• chr11-81785217-C-A
• rs7927911
• ENST00000728684.1:n.134+147C>A

Variant summary

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

The ENST00000728684.1(ENSG00000295219):​n.134+147C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,106 control chromosomes in the GnomAD database, including 4,039 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 0.23 (4039 hom., cov: 32)
• Consequence: ENSG00000295219 ENST00000728684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 4 publications found

Genes affected

ENSG00000295219 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728684.1. 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
	ENSG00000295219	ENST00000728684.1		n.134+147C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34506 AN: 151988 Hom.: 4043 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.227 AC: 34520 AN: 152106 Hom.: 4039 Cov.: 32 AF XY: 0.229 AC XY: 17013 AN XY: 74392

African (AFR) AF: 0.223 AC: 9231 AN: 41472

American (AMR) AF: 0.215 AC: 3282 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3464

East Asian (EAS) AF: 0.183 AC: 948 AN: 5172

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10596

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15213 AN: 67984

Other (OTH) AF: 0.248 AC: 525 AN: 2116

Alfa AF: 0.233 Hom.: 2496

Bravo AF: 0.224

Asia WGS AF: 0.314 AC: 1090 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.14

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: rs7927911;

hg19: chr11-81496259;

COSMIC: COSV107158648;