rs9788716

Variant names:

• chr15-47847451-A-C
• rs9788716
• ENST00000662551.1:n.188+34535A>C

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+34535A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,286 control chromosomes in the GnomAD database, including 972 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 0.095 (972 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662551.1. 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
	ENSG00000259754	ENST00000662551.1		n.188+34535A>C		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+34535A>C		intron	N/A
	ENSG00000259754	ENST00000665188.1		n.68+34535A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14394 AN: 152168 Hom.: 974 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0946 AC: 14400 AN: 152286 Hom.: 972 Cov.: 32 AF XY: 0.0972 AC XY: 7238 AN XY: 74450

African (AFR) AF: 0.0495 AC: 2057 AN: 41562

American (AMR) AF: 0.135 AC: 2069 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1682 AN: 5166

South Asian (SAS) AF: 0.132 AC: 638 AN: 4828

European-Finnish (FIN) AF: 0.149 AC: 1583 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5934 AN: 68030

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0879 Hom.: 95

Bravo AF: 0.0936

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.78
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: rs9788716;

hg19: chr15-48139648;