rs7686284

Variant names:

• chr4-44153897-G-A
• rs7686284

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 0.27 in 151,714 control chromosomes in the GnomAD database, including 5,889 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 0.27 (5889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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: 0.270 AC: 40876 AN: 151596 Hom.: 5870 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.270 AC: 40953 AN: 151714 Hom.: 5889 Cov.: 32 AF XY: 0.272 AC XY: 20194 AN XY: 74128

African (AFR) AF: 0.340 AC: 14063 AN: 41392

American (AMR) AF: 0.271 AC: 4130 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2547 AN: 5144

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4816

European-Finnish (FIN) AF: 0.221 AC: 2328 AN: 10544

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14870 AN: 67812

Other (OTH) AF: 0.257 AC: 542 AN: 2106

Alfa AF: 0.241 Hom.: 2398

Bravo AF: 0.280

Asia WGS AF: 0.380 AC: 1319 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7686284; hg19: chr4-44155914;