rs7068170

Variant names:

• chr10-124389020-C-T
• rs7068170

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 0.274 in 152,174 control chromosomes in the GnomAD database, including 5,842 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 0.27 (5842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 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: 0.274 AC: 41636 AN: 152056 Hom.: 5843 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.274 AC: 41653 AN: 152174 Hom.: 5842 Cov.: 33 AF XY: 0.272 AC XY: 20203 AN XY: 74412

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.294

Alfa AF: 0.286 Hom.: 1245

Bravo AF: 0.275

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7068170; hg19: chr10-126077589;