chr10-121645966-C-G

Position:

• chr10-121645966-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;