chr16-16864058-G-A

Variant names:

• chr16-16864058-G-A
• rs7186128
• ENST00000787165.1:n.212-5182G>A

Variant summary

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

The ENST00000787165.1(ENSG00000302475):​n.212-5182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 150,160 control chromosomes in the GnomAD database, including 36,965 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 0.70 (36965 hom., cov: 27)
• Consequence: ENSG00000302475 ENST00000787165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 10 publications found

Genes affected

ENSG00000302475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302475	ENST00000787165.1	n.212-5182G>A		intron_variant	Intron 3 of 3
ENSG00000302475	ENST00000787171.1	n.188-555G>A		intron_variant	Intron 2 of 2
ENSG00000302475	ENST00000787173.1	n.255-555G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.701 AC: 105191 AN: 150058 Hom.: 36937 Cov.: 27

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.701 AC: 105268 AN: 150160 Hom.: 36965 Cov.: 27 AF XY: 0.696 AC XY: 50866 AN XY: 73104

African (AFR) AF: 0.700 AC: 28409 AN: 40602

American (AMR) AF: 0.701 AC: 10579 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2410 AN: 3464

East Asian (EAS) AF: 0.796 AC: 4069 AN: 5110

South Asian (SAS) AF: 0.650 AC: 3101 AN: 4768

European-Finnish (FIN) AF: 0.625 AC: 6241 AN: 9992

Middle Eastern (MID) AF: 0.648 AC: 188 AN: 290

European-Non Finnish (NFE) AF: 0.710 AC: 48140 AN: 67836

Other (OTH) AF: 0.703 AC: 1472 AN: 2094

Alfa AF: 0.705 Hom.: 87677

Bravo AF: 0.704

Asia WGS AF: 0.708 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7186128; hg19: chr16-16957915;