rs822387

Variant names:

• chr3-186838248-T-C
• rs822387

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 0.145 in 152,226 control chromosomes in the GnomAD database, including 2,622 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 0.14 (2622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 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: 0.145 AC: 22005 AN: 152108 Hom.: 2615 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.145 AC: 22028 AN: 152226 Hom.: 2622 Cov.: 32 AF XY: 0.141 AC XY: 10476 AN XY: 74454

African (AFR) AF: 0.320 AC: 13275 AN: 41468

American (AMR) AF: 0.108 AC: 1645 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3468

East Asian (EAS) AF: 0.0355 AC: 184 AN: 5188

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4834

European-Finnish (FIN) AF: 0.0497 AC: 528 AN: 10618

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5522 AN: 68032

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.110 Hom.: 3119

Bravo AF: 0.159

Asia WGS AF: 0.0500 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.7
DANN	Benign	0.91
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs822387; hg19: chr3-186556037;