rs30882

Variant names:

• chr16-62965569-T-C
• rs30882
• ENST00000734827.1:n.62-42789A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-62965569-T-C
• chr16-62965569-T-G

Variant summary

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

The ENST00000734827.1(ENSG00000260658):​n.62-42789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,148 control chromosomes in the GnomAD database, including 2,709 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 0.18 (2709 hom., cov: 32)
• Consequence: ENSG00000260658 ENST00000734827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 3 publications found

Genes affected

ENSG00000260658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734827.1. 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
	ENSG00000260658	ENST00000734827.1		n.62-42789A>G		intron	N/A
	ENSG00000260658	ENST00000734828.1		n.176-42789A>G		intron	N/A
	ENSG00000260658	ENST00000734829.1		n.57-42789A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27071 AN: 152030 Hom.: 2708 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.178 AC: 27080 AN: 152148 Hom.: 2709 Cov.: 32 AF XY: 0.179 AC XY: 13305 AN XY: 74388

African (AFR) AF: 0.0876 AC: 3639 AN: 41526

American (AMR) AF: 0.212 AC: 3236 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1244 AN: 5144

South Asian (SAS) AF: 0.178 AC: 858 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1910 AN: 10590

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14839 AN: 67994

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.200 Hom.: 4077

Bravo AF: 0.178

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-0.37

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: rs30882;

hg19: chr16-62999473;