8-60890428-C-G

Position:

• chr8-60890428-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 0.796 in 152,176 control chromosomes in the GnomAD database, including 48,380 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 0.80 (48380 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60890428C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287975	ENST00000658608.1	n.357+5278C>G		intron_variant
ENSG00000287975	ENST00000668199.1	n.756+5278C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121106 AN: 152058 Hom.: 48344 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.796 AC: 121201 AN: 152176 Hom.: 48380 Cov.: 32 AF XY: 0.794 AC XY: 59093 AN XY: 74384

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.806

Alfa AF: 0.755 Hom.: 2268

Bravo AF: 0.803

Asia WGS AF: 0.754 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237043; hg19: chr8-61802987;