rs8177600

Positions:

• chr10-5983100-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.00694

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.360

Alfa AF: 0.388 Hom.: 5487

Bravo AF: 0.336

Asia WGS AF: 0.124 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177600; hg19: chr10-6025063;