ENST00000849660.1:n.57-3287A>G

Variant names:

• chr16-49418176-T-C
• rs16947390
• ENST00000849660.1:n.57-3287A>G

Variant summary

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

The ENST00000849660.1(ENSG00000262950):​n.57-3287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,194 control chromosomes in the GnomAD database, including 635 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 0.074 (635 hom., cov: 32)
• Consequence: ENSG00000262950 ENST00000849660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 2 publications found

Genes affected

ENSG00000262950 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849660.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262950	ENST00000849660.1		n.57-3287A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11189 AN: 152076 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0736 AC: 11199 AN: 152194 Hom.: 635 Cov.: 32 AF XY: 0.0707 AC XY: 5264 AN XY: 74406

African (AFR) AF: 0.152 AC: 6324 AN: 41524

American (AMR) AF: 0.0489 AC: 748 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5168

South Asian (SAS) AF: 0.0820 AC: 395 AN: 4818

European-Finnish (FIN) AF: 0.0267 AC: 283 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3042 AN: 67992

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0664 Hom.: 75

Bravo AF: 0.0768

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs16947390; hg19: chr16-49452087;