chr16-31258230-C-T

Variant names:

• chr16-31258230-C-T
• rs8057320
• ENST00000849228.1:n.*211C>T

Variant summary

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

The ENST00000849228.1(ENSG00000310348):​n.*211C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 147,426 control chromosomes in the GnomAD database, including 29,891 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 0.63 (29891 hom., cov: 25)
• Consequence: ENSG00000310348 ENST00000849228.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 9 publications found

Genes affected

ENSG00000310348 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849228.1. 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
	ENSG00000310348	ENST00000849228.1		n.*211C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.631 AC: 92929 AN: 147362 Hom.: 29893 Cov.: 25

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.630 AC: 92944 AN: 147426 Hom.: 29891 Cov.: 25 AF XY: 0.626 AC XY: 44907 AN XY: 71712

African (AFR) AF: 0.519 AC: 20450 AN: 39380

American (AMR) AF: 0.633 AC: 9362 AN: 14784

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2696 AN: 3464

East Asian (EAS) AF: 0.716 AC: 3658 AN: 5112

South Asian (SAS) AF: 0.459 AC: 2183 AN: 4754

European-Finnish (FIN) AF: 0.619 AC: 5691 AN: 9194

Middle Eastern (MID) AF: 0.853 AC: 237 AN: 278

European-Non Finnish (NFE) AF: 0.692 AC: 46698 AN: 67502

Other (OTH) AF: 0.684 AC: 1403 AN: 2052

Alfa AF: 0.685 Hom.: 41053

Bravo AF: 0.629

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.46
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs8057320; hg19: chr16-31269551;