rs6990097

Variant names:

• chr8-9555347-T-C
• rs6990097

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 0.284 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
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.278 AC: 5 AN: 18

European-Finnish (FIN) AF: 0.100 AC: 1 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 3 AN: 18

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.304 AC: 12622 AN: 41466

American (AMR) AF: 0.227 AC: 3466 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2155 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4299 AN: 10536

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17588 AN: 67972

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.257 Hom.: 6765

Bravo AF: 0.271

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6990097; hg19: chr8-9412857;