rs6801526

Positions:

• chr3-143217030-G-A

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 0.0861 in 152,190 control chromosomes in the GnomAD database, including 693 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 0.086 (693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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: 0.0860 AC: 13083 AN: 152072 Hom.: 688 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0861 AC: 13097 AN: 152190 Hom.: 693 Cov.: 32 AF XY: 0.0869 AC XY: 6464 AN XY: 74402

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0695 Hom.: 248

Bravo AF: 0.0947

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.078
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6801526; hg19: chr3-142935872;