rs807846

Positions:

• chr6-21297845-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 0.609 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.591

Alfa AF: 0.565 Hom.: 33390

Bravo AF: 0.613

Asia WGS AF: 0.774 AC: 2692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807846; hg19: chr6-21298076;