rs1973172

chr5-100302184-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.246 in 151,304 control chromosomes in the GnomAD database, including 4,906 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 0.25 (4906 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37154 AN: 151184 Hom.: 4895 Cov.: 30

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.246 AC: 37209 AN: 151304 Hom.: 4906 Cov.: 30 AF XY: 0.243 AC XY: 17958 AN XY: 73950

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.0975

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.287

Alfa AF: 0.263 Hom.: 10411

Bravo AF: 0.262

Asia WGS AF: 0.0890 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1973172; hg19: chr5-99637888;