rs10107657

Positions:

• chr8-55627676-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 0.236 in 152,032 control chromosomes in the GnomAD database, including 4,922 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 0.24 (4922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35806 AN: 151914 Hom.: 4892 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.236 AC: 35894 AN: 152032 Hom.: 4922 Cov.: 32 AF XY: 0.236 AC XY: 17528 AN XY: 74324

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.213

Alfa AF: 0.196 Hom.: 6470

Bravo AF: 0.234

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10107657; hg19: chr8-56540235;