rs6996198

Variant names:

• chr8-64550885-C-T
• rs6996198

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 0.179 in 152,034 control chromosomes in the GnomAD database, including 2,477 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 0.18 (2477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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: 0.179 AC: 27212 AN: 151916 Hom.: 2466 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.179 AC: 27262 AN: 152034 Hom.: 2477 Cov.: 32 AF XY: 0.181 AC XY: 13474 AN XY: 74302

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.180

Alfa AF: 0.164 Hom.: 4252

Bravo AF: 0.178

Asia WGS AF: 0.191 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6996198; hg19: chr8-65463442;