rs7703173

Variant names:

• chr5-52465396-T-A
• rs7703173

Your query was ambiguous. Multiple possible variants found:

• chr5-52465396-T-A
• chr5-52465396-T-C

Variant summary

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

The variant allele was found at a frequency of 0.173 in 152,242 control chromosomes in the GnomAD database, including 2,334 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 (2334 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26298 AN: 152124 Hom.: 2321 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.173 AC: 26343 AN: 152242 Hom.: 2334 Cov.: 33 AF XY: 0.170 AC XY: 12651 AN XY: 74448

African (AFR) AF: 0.206 AC: 8569 AN: 41538

American (AMR) AF: 0.139 AC: 2128 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3468

East Asian (EAS) AF: 0.125 AC: 649 AN: 5184

South Asian (SAS) AF: 0.190 AC: 918 AN: 4830

European-Finnish (FIN) AF: 0.128 AC: 1359 AN: 10624

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

European-Non Finnish (NFE) AF: 0.172 AC: 11676 AN: 67986

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.0832 Hom.: 119

Bravo AF: 0.172

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs7703173; hg19: chr5-51761230;