16-86674163-G-A

Variant names:

• chr16-86674163-G-A
• rs7188801
• ENST00000808928.1:n.855-22010G>A

Variant summary

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

The ENST00000808928.1(ENSG00000261161):​n.855-22010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 131,306 control chromosomes in the GnomAD database, including 2,643 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 0.21 (2643 hom., cov: 26)
• Consequence: ENSG00000261161 ENST00000808928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 6 publications found

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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
ENSG00000261161	ENST00000808928.1	n.855-22010G>A		intron_variant	Intron 4 of 4
ENSG00000261161	ENST00000808929.1	n.722-22010G>A		intron_variant	Intron 5 of 5
ENSG00000261161	ENST00000808930.1	n.114-22010G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 27162 AN: 131162 Hom.: 2639 Cov.: 26

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.207 AC: 27190 AN: 131306 Hom.: 2643 Cov.: 26 AF XY: 0.207 AC XY: 13177 AN XY: 63518

African (AFR) AF: 0.251 AC: 8727 AN: 34788

American (AMR) AF: 0.145 AC: 1873 AN: 12948

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 642 AN: 3228

East Asian (EAS) AF: 0.381 AC: 1646 AN: 4316

South Asian (SAS) AF: 0.228 AC: 890 AN: 3902

European-Finnish (FIN) AF: 0.226 AC: 1866 AN: 8250

Middle Eastern (MID) AF: 0.309 AC: 50 AN: 162

European-Non Finnish (NFE) AF: 0.179 AC: 10923 AN: 61060

Other (OTH) AF: 0.189 AC: 344 AN: 1824

Alfa AF: 0.164 Hom.: 1045

Bravo AF: 0.180

Asia WGS AF: 0.240 AC: 833 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	0.12
DANN	Benign	0.25
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7188801; hg19: chr16-86707769;