rs6990097

Variant names:

• chr8-9555347-T-C
• rs6990097

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 0.284 in 152,058 control chromosomes in the GnomAD database, including 6,354 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 0.28 (6352 hom., cov: 32)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.284 AC: 43128 AN: 151892 Hom.: 6332 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.188 AC: 9 AN: 48 Hom.: 2 Cov.: 0 AF XY: 0.167 AC XY: 5 AN XY: 30

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.284 AC: 43187 AN: 152010 Hom.: 6352 Cov.: 32 AF XY: 0.290 AC XY: 21538 AN XY: 74300

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.249

Alfa AF: 0.255 Hom.: 5109

Bravo AF: 0.271

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6990097; hg19: chr8-9412857;