chr6-21297845-T-C

Variant names:

• chr6-21297845-T-C
• rs807846

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 0.609 in 152,050 control chromosomes in the GnomAD database, including 28,606 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 0.61 (28606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 5 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 = 0.79 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92468 AN: 151932 Hom.: 28579 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.609 AC: 92546 AN: 152050 Hom.: 28606 Cov.: 32 AF XY: 0.615 AC XY: 45691 AN XY: 74298

African (AFR) AF: 0.676 AC: 28062 AN: 41492

American (AMR) AF: 0.623 AC: 9504 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4191 AN: 5172

South Asian (SAS) AF: 0.778 AC: 3752 AN: 4822

European-Finnish (FIN) AF: 0.561 AC: 5917 AN: 10540

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36925 AN: 67972

Other (OTH) AF: 0.591 AC: 1248 AN: 2110

Alfa AF: 0.568 Hom.: 41968

Bravo AF: 0.613

Asia WGS AF: 0.774 AC: 2692 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	1.4
DANN	Benign	0.20
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs807846; hg19: chr6-21298076;