rs6998277

chr8-102627713-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 0.262 in 152,022 control chromosomes in the GnomAD database, including 6,238 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 0.26 (6238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39817 AN: 151904 Hom.: 6220 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.262 AC: 39887 AN: 152022 Hom.: 6238 Cov.: 32 AF XY: 0.259 AC XY: 19221 AN XY: 74318

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.231

Alfa AF: 0.201 Hom.: 3038

Bravo AF: 0.267

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6998277; hg19: chr8-103639941;