10-28738294-A-G

Position:

• chr10-28738294-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 0.139 in 152,116 control chromosomes in the GnomAD database, including 1,971 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 0.14 (1971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.139 AC: 21067 AN: 151998 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.139 AC: 21088 AN: 152116 Hom.: 1971 Cov.: 32 AF XY: 0.134 AC XY: 9978 AN XY: 74390

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0728

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.120

Alfa AF: 0.105 Hom.: 1031

Bravo AF: 0.144

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.83
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1248993; hg19: chr10-29027223;