rs10055210

Variant names:

• chr5-118708301-T-C
• rs10055210

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 0.292 in 151,952 control chromosomes in the GnomAD database, including 6,671 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 (6671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44268 AN: 151834 Hom.: 6666 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.292 AC: 44298 AN: 151952 Hom.: 6671 Cov.: 32 AF XY: 0.295 AC XY: 21930 AN XY: 74270

African (AFR) AF: 0.367 AC: 15221 AN: 41420

American (AMR) AF: 0.283 AC: 4314 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2097 AN: 5162

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2482 AN: 10560

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16514 AN: 67942

Other (OTH) AF: 0.295 AC: 622 AN: 2108

Alfa AF: 0.258 Hom.: 2823

Bravo AF: 0.295

Asia WGS AF: 0.365 AC: 1267 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.50
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10055210;

hg19: chr5-118043996;