8-89863690-T-C

Position:

• chr8-89863690-T-C

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 0.288 in 151,974 control chromosomes in the GnomAD database, including 6,685 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 0.29 (6685 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.89863690T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43655 AN: 151856 Hom.: 6675 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.288 AC: 43698 AN: 151974 Hom.: 6685 Cov.: 32 AF XY: 0.282 AC XY: 20945 AN XY: 74274

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.300

Alfa AF: 0.256 Hom.: 2450

Bravo AF: 0.293

Asia WGS AF: 0.209 AC: 725 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.2
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7015630; hg19: chr8-90875918;