rs6478106

Variant names:

• chr9-114783386-C-T
• rs6478106

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 0.336 in 152,044 control chromosomes in the GnomAD database, including 8,950 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 0.34 (8950 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.336 AC: 50999 AN: 151926 Hom.: 8932 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.336 AC: 51067 AN: 152044 Hom.: 8950 Cov.: 32 AF XY: 0.341 AC XY: 25366 AN XY: 74296

African (AFR) AF: 0.411 AC: 17048 AN: 41468

American (AMR) AF: 0.371 AC: 5671 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1571 AN: 5180

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3918 AN: 10530

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19452 AN: 67980

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.304 Hom.: 24031

Bravo AF: 0.339

Asia WGS AF: 0.366 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.31
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6478106; hg19: chr9-117545666;