5-173237160-G-A

Variant names:

• chr5-173237160-G-A
• rs6882776

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 0.34 in 152,214 control chromosomes in the GnomAD database, including 9,234 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 0.34 (9234 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51680 AN: 152096 Hom.: 9233 Cov.: 34

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51716 AN: 152214 Hom.: 9234 Cov.: 34 AF XY: 0.350 AC XY: 26022 AN XY: 74418

African (AFR) AF: 0.342 AC: 14216 AN: 41544

American (AMR) AF: 0.431 AC: 6600 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3296 AN: 5176

South Asian (SAS) AF: 0.399 AC: 1929 AN: 4832

European-Finnish (FIN) AF: 0.428 AC: 4533 AN: 10586

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19242 AN: 67980

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.308 Hom.: 29540

Bravo AF: 0.344

Asia WGS AF: 0.502 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6882776; hg19: chr5-172664163;