rs6990097

chr8-9555347-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 0.284 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;