rs6904416

Variant names:

• chr6-98542613-T-C
• rs6904416

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 0.122 in 152,232 control chromosomes in the GnomAD database, including 1,497 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 0.12 (1497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18568 AN: 152114 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.122 AC: 18561 AN: 152232 Hom.: 1497 Cov.: 32 AF XY: 0.120 AC XY: 8914 AN XY: 74430

African (AFR) AF: 0.0324 AC: 1345 AN: 41558

American (AMR) AF: 0.106 AC: 1616 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3468

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5178

South Asian (SAS) AF: 0.132 AC: 636 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1719 AN: 10606

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.175 AC: 11870 AN: 68002

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.155 Hom.: 5710

Bravo AF: 0.113

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.3
DANN	Benign	0.60
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6904416; hg19: chr6-98990489;