rs10107657

Variant names:

• chr8-55627676-T-C
• rs10107657

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 0.236 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.378 AC: 15679 AN: 41452

American (AMR) AF: 0.147 AC: 2245 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 789 AN: 3466

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5174

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4820

European-Finnish (FIN) AF: 0.212 AC: 2242 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12762 AN: 67970

Other (OTH) AF: 0.213 AC: 450 AN: 2108

Alfa AF: 0.201 Hom.: 14604

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs10107657; hg19: chr8-56540235;