10-121645966-C-G

Variant names:

• chr10-121645966-C-G
• rs7902581

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 0.338 in 151,928 control chromosomes in the GnomAD database, including 9,551 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 0.34 (9551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.338 AC: 51325 AN: 151810 Hom.: 9539 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.338 AC: 51374 AN: 151928 Hom.: 9551 Cov.: 31 AF XY: 0.335 AC XY: 24871 AN XY: 74276

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.333

Alfa AF: 0.153 Hom.: 258

Bravo AF: 0.346

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902581; hg19: chr10-123405480;