rs7103224

Positions:

• chr11-116793250-G-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 0.0602 in 152,018 control chromosomes in the GnomAD database, including 470 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 0.060 (470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 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: 0.0604 AC: 9171 AN: 151900 Hom.: 471 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0714

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0602 AC: 9158 AN: 152018 Hom.: 470 Cov.: 32 AF XY: 0.0640 AC XY: 4755 AN XY: 74288

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0401

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0630 Hom.: 42

Bravo AF: 0.0511

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.84
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7103224; hg19: chr11-116663966;