16-27378090-G-A

Variant names:

• chr16-27378090-G-A
• rs7191188
• ENST00000722344.1:n.77-83G>A

Variant summary

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

The ENST00000722344.1(ENSG00000294275):​n.77-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,058 control chromosomes in the GnomAD database, including 8,895 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 0.32 (8895 hom., cov: 32)
• Consequence: ENSG00000294275 ENST00000722344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 9 publications found

Genes affected

ENSG00000294275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722344.1. 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
	ENSG00000294275	ENST00000722344.1		n.77-83G>A		intron	N/A
	ENSG00000294275	ENST00000722345.1		n.173+28G>A		intron	N/A
	ENSG00000294275	ENST00000722346.1		n.28-83G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48070 AN: 151940 Hom.: 8874 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.317 AC: 48131 AN: 152058 Hom.: 8895 Cov.: 32 AF XY: 0.312 AC XY: 23214 AN XY: 74330

African (AFR) AF: 0.518 AC: 21490 AN: 41448

American (AMR) AF: 0.234 AC: 3571 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3466

East Asian (EAS) AF: 0.200 AC: 1035 AN: 5176

South Asian (SAS) AF: 0.130 AC: 627 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10578

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16552 AN: 67960

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.260 Hom.: 26349

Bravo AF: 0.323

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.62
PhyloP100		0.29

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: rs7191188;

hg19: chr16-27389411;