rs7228082

Positions:

• chr18-3406935-T-C

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 0.166 in 437,108 control chromosomes in the GnomAD database, including 9,043 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 0.22 (5354 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3689 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33820 AN: 152042 Hom.: 5338 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.135 AC: 38530 AN: 284948 Hom.: 3689 AF XY: 0.130 AC XY: 19972 AN XY: 153482

Gnomad4 AFR exome AF: 0.433

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.140

Gnomad4 SAS exome AF: 0.0852

Gnomad4 FIN exome AF: 0.0896

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.223 AC: 33875 AN: 152160 Hom.: 5354 Cov.: 32 AF XY: 0.221 AC XY: 16427 AN XY: 74410

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0920

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.222

Alfa AF: 0.155 Hom.: 2364

Bravo AF: 0.254

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7228082; hg19: chr18-3406933;