rs9302755

Variant names:

• chr16-51075728-A-C
• rs9302755
• ENST00000785664.1:n.408-13316T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-51075728-A-C
• chr16-51075728-A-T

Variant summary

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

The ENST00000785664.1(ENSG00000287718):​n.408-13316T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,146 control chromosomes in the GnomAD database, including 32,839 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 0.65 (32839 hom., cov: 33)
• Consequence: ENSG00000287718 ENST00000785664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 4 publications found

Genes affected

ENSG00000287718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785664.1. 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
	ENSG00000287718	ENST00000785664.1		n.408-13316T>G		intron	N/A
	ENSG00000287718	ENST00000785665.1		n.516+5601T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98726 AN: 152028 Hom.: 32778 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.650 AC: 98850 AN: 152146 Hom.: 32839 Cov.: 33 AF XY: 0.648 AC XY: 48199 AN XY: 74368

African (AFR) AF: 0.778 AC: 32297 AN: 41524

American (AMR) AF: 0.648 AC: 9916 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2253 AN: 3470

East Asian (EAS) AF: 0.811 AC: 4192 AN: 5172

South Asian (SAS) AF: 0.611 AC: 2948 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5693 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39429 AN: 67974

Other (OTH) AF: 0.667 AC: 1408 AN: 2110

Alfa AF: 0.611 Hom.: 123509

Bravo AF: 0.669

Asia WGS AF: 0.751 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.52
PhyloP100		-0.58

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: rs9302755;

hg19: chr16-51109639;