rs1106683

chr7-131768766-G-Achr7-131768766-G-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 0.143 in 152,218 control chromosomes in the GnomAD database, including 1,634 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 0.14 (1634 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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: 0.143 AC: 21741 AN: 152100 Hom.: 1635 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.143 AC: 21755 AN: 152218 Hom.: 1634 Cov.: 33 AF XY: 0.144 AC XY: 10681 AN XY: 74410

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.123

Alfa AF: 0.137 Hom.: 2690

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.93
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1106683; hg19: chr7-131453525;