16-52550261-A-G

Variant names:

• chr16-52550261-A-G
• rs3095606
• ENST00000826650.1:n.102+3749A>G

Variant summary

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

The ENST00000826650.1(ENSG00000285800):​n.102+3749A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,034 control chromosomes in the GnomAD database, including 9,898 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 0.35 (9898 hom., cov: 32)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 3 publications found

Genes affected

ENSG00000285800 (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 (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826650.1. 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
	ENSG00000285800	ENST00000826650.1		n.102+3749A>G		intron	N/A
	ENSG00000285800	ENST00000826651.1		n.89+3749A>G		intron	N/A
	ENSG00000285800	ENST00000826652.1		n.104+3701A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52934 AN: 151916 Hom.: 9872 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.349 AC: 53020 AN: 152034 Hom.: 9898 Cov.: 32 AF XY: 0.352 AC XY: 26157 AN XY: 74308

African (AFR) AF: 0.452 AC: 18755 AN: 41478

American (AMR) AF: 0.378 AC: 5769 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3196 AN: 5158

South Asian (SAS) AF: 0.266 AC: 1281 AN: 4816

European-Finnish (FIN) AF: 0.318 AC: 3350 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18186 AN: 67982

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.295 Hom.: 1901

Bravo AF: 0.362

Asia WGS AF: 0.429 AC: 1493 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	1.1
DANN	Benign	0.42
PhyloP100		-0.092

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: rs3095606;

hg19: chr16-52584173;

COSMIC: COSV54867858;