10-5983100-T-C

Variant names:

• chr10-5983100-T-C
• rs8177600

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 0.332 in 152,148 control chromosomes in the GnomAD database, including 9,425 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 0.33 (9425 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50545 AN: 152030 Hom.: 9423 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.00711

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.332 AC: 50566 AN: 152148 Hom.: 9425 Cov.: 33 AF XY: 0.323 AC XY: 24001 AN XY: 74384

African (AFR) AF: 0.225 AC: 9337 AN: 41506

American (AMR) AF: 0.349 AC: 5337 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3472

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5190

South Asian (SAS) AF: 0.252 AC: 1218 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3146 AN: 10582

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28424 AN: 67978

Other (OTH) AF: 0.360 AC: 762 AN: 2114

Alfa AF: 0.391 Hom.: 6225

Bravo AF: 0.336

Asia WGS AF: 0.124 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs8177600; hg19: chr10-6025063;