rs4703820

Variant names:

• chr5-80917997-A-G
• rs4703820
• XR_001742759.2:n.13595A>G

Variant summary

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

The XR_001742759.2(LOC107986428):​n.13595A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,174 control chromosomes in the GnomAD database, including 3,212 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 0.19 (3212 hom., cov: 32)
• Consequence: LOC107986428 XR_001742759.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 4 publications found

Genes affected

LOC107986428 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29429 AN: 152054 Hom.: 3208 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.194 AC: 29453 AN: 152174 Hom.: 3212 Cov.: 32 AF XY: 0.194 AC XY: 14454 AN XY: 74404

African (AFR) AF: 0.266 AC: 11049 AN: 41508

American (AMR) AF: 0.258 AC: 3938 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5176

South Asian (SAS) AF: 0.158 AC: 762 AN: 4822

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10608

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

European-Non Finnish (NFE) AF: 0.135 AC: 9206 AN: 68000

Other (OTH) AF: 0.205 AC: 433 AN: 2112

Alfa AF: 0.165 Hom.: 7661

Bravo AF: 0.215

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.85
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs4703820; hg19: chr5-80213816;