rs6788482

Variant names:

• chr3-110322685-G-A
• rs6788482

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 0.149 in 151,936 control chromosomes in the GnomAD database, including 3,029 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 0.15 (3029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.149 AC: 22656 AN: 151818 Hom.: 3024 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.149 AC: 22683 AN: 151936 Hom.: 3029 Cov.: 32 AF XY: 0.147 AC XY: 10929 AN XY: 74264

African (AFR) AF: 0.350 AC: 14471 AN: 41374

American (AMR) AF: 0.152 AC: 2322 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5166

South Asian (SAS) AF: 0.108 AC: 523 AN: 4822

European-Finnish (FIN) AF: 0.0343 AC: 362 AN: 10546

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3127 AN: 67964

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.114 Hom.: 289

Bravo AF: 0.170

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.46
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs6788482; hg19: chr3-110041532;