rs830907

Variant names:

• chr5-52608773-G-A
• rs830907

Your query was ambiguous. Multiple possible variants found:

• chr5-52608773-G-A
• chr5-52608773-G-T

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 0.354 in 151,554 control chromosomes in the GnomAD database, including 11,124 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 0.35 (11124 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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: 0.354 AC: 53567 AN: 151436 Hom.: 11122 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.354 AC: 53579 AN: 151554 Hom.: 11124 Cov.: 31 AF XY: 0.353 AC XY: 26154 AN XY: 73998

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.377

Alfa AF: 0.433 Hom.: 7000

Bravo AF: 0.336

Asia WGS AF: 0.286 AC: 997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs830907; hg19: chr5-51904607; COSMIC: COSV60130024;