chr8-27481837-T-C

Variant names:

• chr8-27481837-T-C
• rs6558000

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.207 in 152,100 control chromosomes in the GnomAD database, including 6,954 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 0.21 (6954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31464 AN: 151982 Hom.: 6927 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.207 AC: 31530 AN: 152100 Hom.: 6954 Cov.: 32 AF XY: 0.203 AC XY: 15060 AN XY: 74346

African (AFR) AF: 0.558 AC: 23136 AN: 41442

American (AMR) AF: 0.102 AC: 1565 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3466

East Asian (EAS) AF: 0.139 AC: 722 AN: 5180

South Asian (SAS) AF: 0.135 AC: 651 AN: 4822

European-Finnish (FIN) AF: 0.0457 AC: 483 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3966 AN: 68010

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.0950 Hom.: 2260

Bravo AF: 0.225

Asia WGS AF: 0.170 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6558000; hg19: chr8-27339354;