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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.132 AC: 5458 AN: 41406

American (AMR) AF: 0.353 AC: 5352 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1887 AN: 3458

East Asian (EAS) AF: 0.328 AC: 1680 AN: 5126

South Asian (SAS) AF: 0.293 AC: 1407 AN: 4802

European-Finnish (FIN) AF: 0.490 AC: 5158 AN: 10522

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31221 AN: 67758

Other (OTH) AF: 0.377 AC: 794 AN: 2108

Alfa AF: 0.435 Hom.: 7788

Bravo AF: 0.336

Asia WGS AF: 0.286 AC: 997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.39
PhyloP100		-0.031

Splicing

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

Other links and lift over

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