rs10102164

Variant names:

• chr8-54509054-G-A
• rs10102164

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 0.188 in 152,120 control chromosomes in the GnomAD database, including 2,709 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 0.19 (2709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28633 AN: 152000 Hom.: 2710 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.188 AC: 28656 AN: 152120 Hom.: 2709 Cov.: 32 AF XY: 0.190 AC XY: 14090 AN XY: 74350

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.180

Alfa AF: 0.189 Hom.: 3504

Bravo AF: 0.179

Asia WGS AF: 0.270 AC: 939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10102164; hg19: chr8-55421614;