rs999828

Variant names:

• chr5-67979460-C-T
• rs999828
• ENST00000785994.1:n.270+2178G>A

Variant summary

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

The ENST00000785994.1(ENSG00000302346):​n.270+2178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,112 control chromosomes in the GnomAD database, including 2,725 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 0.17 (2725 hom., cov: 33)
• Consequence: ENSG00000302346 ENST00000785994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 3 publications found

Genes affected

ENSG00000302346 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785994.1. 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
	ENSG00000302346	ENST00000785994.1		n.270+2178G>A		intron	N/A
	ENSG00000302346	ENST00000785995.1		n.303+2178G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25941 AN: 151996 Hom.: 2725 Cov.: 33

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.171 AC: 25950 AN: 152112 Hom.: 2725 Cov.: 33 AF XY: 0.171 AC XY: 12718 AN XY: 74386

African (AFR) AF: 0.0813 AC: 3374 AN: 41522

American (AMR) AF: 0.127 AC: 1939 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3472

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5186

South Asian (SAS) AF: 0.105 AC: 507 AN: 4814

European-Finnish (FIN) AF: 0.292 AC: 3089 AN: 10576

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15679 AN: 67952

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.198 Hom.: 2173

Bravo AF: 0.153

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.79
PhyloP100		0.32

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: rs999828;

hg19: chr5-67275288;