chr16-66118898-T-C

Variant names:

• chr16-66118898-T-C
• rs9302579
• ENST00000787386.1:n.674+10240A>G

Variant summary

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

The ENST00000787386.1(ENSG00000302504):​n.674+10240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,256 control chromosomes in the GnomAD database, including 1,450 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 0.082 (1450 hom., cov: 33)
• Consequence: ENSG00000302504 ENST00000787386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 3 publications found

Genes affected

ENSG00000302504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787386.1. 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
	ENSG00000302504	ENST00000787386.1		n.674+10240A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12380 AN: 152138 Hom.: 1446 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00775

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0815 AC: 12416 AN: 152256 Hom.: 1450 Cov.: 33 AF XY: 0.0797 AC XY: 5931 AN XY: 74440

African (AFR) AF: 0.256 AC: 10648 AN: 41518

American (AMR) AF: 0.0578 AC: 884 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5180

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4826

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00775 AC: 527 AN: 68028

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0341 Hom.: 74

Bravo AF: 0.0954

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.69
PhyloP100		-0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9302579; hg19: chr16-66152801;