rs7682027

Positions:

• chr4-68672027-C-T

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 0.189 in 152,060 control chromosomes in the GnomAD database, including 3,322 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 0.19 (3322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28763 AN: 151944 Hom.: 3326 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.189 AC: 28749 AN: 152060 Hom.: 3322 Cov.: 32 AF XY: 0.189 AC XY: 14013 AN XY: 74312

Gnomad4 AFR AF: 0.0497

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.201

Alfa AF: 0.210 Hom.: 482

Bravo AF: 0.188

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7682027; hg19: chr4-69537745;