rs3823288

Variant names:

• chr6-132441256-A-T
• rs3823288

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 0.299 in 151,942 control chromosomes in the GnomAD database, including 8,370 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 0.30 (8370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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: 0.299 AC: 45411 AN: 151824 Hom.: 8346 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.299 AC: 45485 AN: 151942 Hom.: 8370 Cov.: 32 AF XY: 0.301 AC XY: 22368 AN XY: 74274

African (AFR) AF: 0.485 AC: 20094 AN: 41402

American (AMR) AF: 0.361 AC: 5514 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2704 AN: 5154

South Asian (SAS) AF: 0.212 AC: 1020 AN: 4810

European-Finnish (FIN) AF: 0.216 AC: 2287 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12590 AN: 67950

Other (OTH) AF: 0.278 AC: 585 AN: 2104

Alfa AF: 0.250 Hom.: 749

Bravo AF: 0.322

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.51
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs3823288; hg19: chr6-132762395;