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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986428	XR_001742759.2	n.13595A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;