chr5-175357866-G-A

Variant names:

• chr5-175357866-G-A
• rs4868514
• ENST00000820924.1:n.420-2918G>A

Variant summary

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

The ENST00000820924.1(ENSG00000306776):​n.420-2918G>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 152,080 control chromosomes in the GnomAD database, including 2,367 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 (2367 hom., cov: 32)
• Consequence: ENSG00000306776 ENST00000820924.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 1 publications found

Genes affected

ENSG00000306776 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820924.1. 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
	ENSG00000306776	ENST00000820924.1		n.420-2918G>A		intron	N/A
	ENSG00000306776	ENST00000820925.1		n.273-2915G>A		intron	N/A
	ENSG00000306776	ENST00000820926.1		n.273-2918G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25924 AN: 151962 Hom.: 2361 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.171 AC: 25963 AN: 152080 Hom.: 2367 Cov.: 32 AF XY: 0.168 AC XY: 12513 AN XY: 74348

African (AFR) AF: 0.245 AC: 10172 AN: 41468

American (AMR) AF: 0.126 AC: 1934 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3466

East Asian (EAS) AF: 0.112 AC: 579 AN: 5168

South Asian (SAS) AF: 0.112 AC: 540 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1687 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10030 AN: 67972

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.162 Hom.: 1024

Bravo AF: 0.173

Asia WGS AF: 0.138 AC: 481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.58
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4868514; hg19: chr5-174784869;