rs6801526

Variant names:

• chr3-143217030-G-A
• rs6801526

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 0.0861 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.127 AC: 5255 AN: 41494

American (AMR) AF: 0.103 AC: 1574 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.137 AC: 708 AN: 5178

South Asian (SAS) AF: 0.153 AC: 738 AN: 4810

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10604

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4059 AN: 68022

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0703 Hom.: 343

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs6801526; hg19: chr3-142935872;