rs7686284

Variant names:

• chr4-44153897-G-A
• rs7686284

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.270 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

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.257

Alfa AF: 0.242 Hom.: 2177

Bravo AF: 0.280

Asia WGS AF: 0.380 AC: 1319 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7686284; hg19: chr4-44155914;