rs17827067

Positions:

• chr8-60882612-C-T

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 0.0773 in 152,212 control chromosomes in the GnomAD database, including 498 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 0.077 (498 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60882612C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287975	ENST00000668199.1	n.604-2386C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11760 AN: 152094 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0364

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0773 AC: 11769 AN: 152212 Hom.: 498 Cov.: 32 AF XY: 0.0753 AC XY: 5606 AN XY: 74410

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.0614

Gnomad4 ASJ AF: 0.0364

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.0515

Gnomad4 FIN AF: 0.0598

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0756 Hom.: 126

Bravo AF: 0.0796

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17827067; hg19: chr8-61795171;