6-121582824-T-C

Variant names:

• chr6-121582824-T-C
• rs9490327

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 0.962 in 152,176 control chromosomes in the GnomAD database, including 70,667 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 0.96 (70667 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 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: 0.962 AC: 146318 AN: 152058 Hom.: 70617 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.962 AC: 146425 AN: 152176 Hom.: 70667 Cov.: 31 AF XY: 0.964 AC XY: 71721 AN XY: 74408

African (AFR) AF: 0.879 AC: 36495 AN: 41516

American (AMR) AF: 0.976 AC: 14930 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3451 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5145 AN: 5146

South Asian (SAS) AF: 1.00 AC: 4822 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10594 AN: 10596

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67783 AN: 68008

Other (OTH) AF: 0.961 AC: 2029 AN: 2112

Alfa AF: 0.990 Hom.: 39129

Bravo AF: 0.956

Asia WGS AF: 0.992 AC: 3450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.65
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9490327; hg19: chr6-121903970;