chr5-2109787-T-C

Variant names:

• chr5-2109787-T-C
• rs6879627
• ENST00000653000.1:n.1485-4556T>C

Variant summary

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

The NR_171679.1(LOC105374618):​n.2713-4556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,288 control chromosomes in the GnomAD database, including 56,292 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 0.86 (56292 hom., cov: 34)
• Consequence: LOC105374618 NR_171679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 21 publications found

Genes affected

ENSG00000248994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_171679.1. 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
	LOC105374618	NR_171679.1		n.2713-4556T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248994	ENST00000653000.1		n.1485-4556T>C		intron	N/A
	ENSG00000248994	ENST00000658890.1		n.1546-4556T>C		intron	N/A
	ENSG00000248994	ENST00000660496.1		n.1297-4556T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130326 AN: 152170 Hom.: 56246 Cov.: 34

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.856 AC: 130414 AN: 152288 Hom.: 56292 Cov.: 34 AF XY: 0.854 AC XY: 63562 AN XY: 74458

African (AFR) AF: 0.935 AC: 38883 AN: 41574

American (AMR) AF: 0.800 AC: 12239 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3177 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3079 AN: 5176

South Asian (SAS) AF: 0.905 AC: 4370 AN: 4828

European-Finnish (FIN) AF: 0.836 AC: 8858 AN: 10602

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57044 AN: 68022

Other (OTH) AF: 0.853 AC: 1801 AN: 2112

Alfa AF: 0.842 Hom.: 197794

Bravo AF: 0.853

Asia WGS AF: 0.779 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.8
DANN	Benign	0.27
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs6879627; hg19: chr5-2109901;