chr15-68828768-T-G

Position:

• chr15-68828768-T-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 0.936 in 152,280 control chromosomes in the GnomAD database, including 67,164 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 0.94 (67164 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68828768T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPESP1	ENST00000560188.1	n.97+10451T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142475 AN: 152162 Hom.: 67118 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.962

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

GnomAD4 genome AF: 0.936 AC: 142576 AN: 152280 Hom.: 67164 Cov.: 33 AF XY: 0.938 AC XY: 69859 AN XY: 74464

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.960

Alfa AF: 0.960 Hom.: 8723

Bravo AF: 0.929

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs897001; hg19: chr15-69121107;