chr5-10060185-C-A

Variant names:

• chr5-10060185-C-A
• rs16884060

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 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,991 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 0.18 (2991 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.175 AC: 26635 AN: 152054 Hom.: 2986 Cov.: 33

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.175 AC: 26654 AN: 152172 Hom.: 2991 Cov.: 33 AF XY: 0.179 AC XY: 13298 AN XY: 74384

African (AFR) AF: 0.0499 AC: 2073 AN: 41558

American (AMR) AF: 0.164 AC: 2515 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 774 AN: 3462

East Asian (EAS) AF: 0.457 AC: 2367 AN: 5174

South Asian (SAS) AF: 0.298 AC: 1438 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2530 AN: 10554

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14396 AN: 67990

Other (OTH) AF: 0.182 AC: 385 AN: 2112

Alfa AF: 0.198 Hom.: 5462

Bravo AF: 0.162

Asia WGS AF: 0.322 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.2
DANN	Benign	0.81
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs16884060; hg19: chr5-10060297;