rs1106697

Variant names:

• chr7-155880250-G-A
• rs1106697

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 0.12 in 152,172 control chromosomes in the GnomAD database, including 1,193 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 0.12 (1193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18197 AN: 152054 Hom.: 1187 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.120 AC: 18232 AN: 152172 Hom.: 1193 Cov.: 32 AF XY: 0.115 AC XY: 8559 AN XY: 74382

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0948

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.120

Alfa AF: 0.119 Hom.: 1194

Bravo AF: 0.122

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1106697; hg19: chr7-155672944;