6-108010090-A-T

Variant names:

• chr6-108010090-A-T
• rs4946888

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 0.397 in 152,066 control chromosomes in the GnomAD database, including 17,409 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 0.40 (17409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60313 AN: 151946 Hom.: 17349 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.397 AC: 60438 AN: 152066 Hom.: 17409 Cov.: 32 AF XY: 0.396 AC XY: 29460 AN XY: 74338

African (AFR) AF: 0.819 AC: 33974 AN: 41468

American (AMR) AF: 0.324 AC: 4947 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1866 AN: 5162

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10578

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

European-Non Finnish (NFE) AF: 0.209 AC: 14215 AN: 67964

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.149 Hom.: 275

Bravo AF: 0.423

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.52
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4946888; hg19: chr6-108331294; COSMIC: COSV68860252;