rs722317

Variant names:

• chr11-15902016-G-A
• rs722317
• ENST00000786109.1:n.394+1155G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-15902016-G-A
• chr11-15902016-G-C

Variant summary

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

The ENST00000786109.1(ENSG00000289116):​n.394+1155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,194 control chromosomes in the GnomAD database, including 10,199 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 0.33 (10199 hom., cov: 34)
• Consequence: ENSG00000289116 ENST00000786109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 9 publications found

Genes affected

ENSG00000289116 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786109.1. 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
	ENSG00000289116	ENST00000786109.1		n.394+1155G>A		intron	N/A
	ENSG00000302370	ENST00000786200.1		n.-135C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50479 AN: 152076 Hom.: 10204 Cov.: 34

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.332 AC: 50467 AN: 152194 Hom.: 10199 Cov.: 34 AF XY: 0.328 AC XY: 24382 AN XY: 74400

African (AFR) AF: 0.132 AC: 5485 AN: 41530

American (AMR) AF: 0.298 AC: 4560 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5190

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4826

European-Finnish (FIN) AF: 0.430 AC: 4549 AN: 10578

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31603 AN: 67996

Other (OTH) AF: 0.360 AC: 761 AN: 2116

Alfa AF: 0.418 Hom.: 24383

Bravo AF: 0.313

Asia WGS AF: 0.163 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.90
PhyloP100		-0.13

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: rs722317;

hg19: chr11-15923562;