rs7105218

Positions:

• chr11-68454993-C-A

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 0.171 in 152,186 control chromosomes in the GnomAD database, including 2,400 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 0.17 (2400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.171 AC: 26007 AN: 152068 Hom.: 2401 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.171 AC: 26027 AN: 152186 Hom.: 2400 Cov.: 32 AF XY: 0.166 AC XY: 12348 AN XY: 74412

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.176

Alfa AF: 0.156 Hom.: 246

Bravo AF: 0.185

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7105218; hg19: chr11-68222461;