chr10-84668721-A-G

Position:

• chr10-84668721-A-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 0.121 in 152,356 control chromosomes in the GnomAD database, including 1,211 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 0.12 (1211 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.121 AC: 18390 AN: 152238 Hom.: 1213 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18394 AN: 152356 Hom.: 1211 Cov.: 33 AF XY: 0.119 AC XY: 8850 AN XY: 74508

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0681

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.121

Alfa AF: 0.126 Hom.: 792

Bravo AF: 0.123

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17103805; hg19: chr10-86428477;