5-2403971-A-G

Variant names:

• chr5-2403971-A-G
• rs10052956

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 0.286 in 152,050 control chromosomes in the GnomAD database, including 6,392 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 0.29 (6392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.286 AC: 43442 AN: 151932 Hom.: 6385 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.286 AC: 43472 AN: 152050 Hom.: 6392 Cov.: 32 AF XY: 0.288 AC XY: 21389 AN XY: 74316

African (AFR) AF: 0.333 AC: 13803 AN: 41488

American (AMR) AF: 0.246 AC: 3766 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1025 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1076 AN: 5156

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4818

European-Finnish (FIN) AF: 0.287 AC: 3036 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18330 AN: 67960

Other (OTH) AF: 0.260 AC: 547 AN: 2104

Alfa AF: 0.261 Hom.: 2851

Bravo AF: 0.279

Asia WGS AF: 0.293 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.52
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10052956; hg19: chr5-2404085;