16-742190-A-G

Variant names:

• chr16-742190-A-G
• rs11648796
• ENST00000809713.1:n.87-60A>G

Variant summary

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

The ENST00000809713.1(ENSG00000305233):​n.87-60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,928 control chromosomes in the GnomAD database, including 12,913 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 0.38 (12913 hom., cov: 33)
• Consequence: ENSG00000305233 ENST00000809713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 43 publications found

Genes affected

ENSG00000305233 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809713.1. 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
	ENSG00000305233	ENST00000809713.1		n.87-60A>G		intron	N/A
	ENSG00000305233	ENST00000809714.1		n.209-60A>G		intron	N/A
	ENSG00000305233	ENST00000809715.1		n.281-60A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57198 AN: 151810 Hom.: 12892 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.377 AC: 57274 AN: 151928 Hom.: 12913 Cov.: 33 AF XY: 0.388 AC XY: 28801 AN XY: 74266

African (AFR) AF: 0.543 AC: 22489 AN: 41380

American (AMR) AF: 0.455 AC: 6933 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3468

East Asian (EAS) AF: 0.803 AC: 4150 AN: 5170

South Asian (SAS) AF: 0.486 AC: 2346 AN: 4826

European-Finnish (FIN) AF: 0.346 AC: 3649 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15993 AN: 67970

Other (OTH) AF: 0.323 AC: 682 AN: 2110

Alfa AF: 0.320 Hom.: 1121

Bravo AF: 0.393

Asia WGS AF: 0.601 AC: 2085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.094
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs11648796; hg19: chr16-792190;