rs1107618

Variant names:

• chr7-55212590-G-A
• rs1107618

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 0.348 in 152,136 control chromosomes in the GnomAD database, including 11,645 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 0.35 (11645 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

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 (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.347 AC: 52800 AN: 152018 Hom.: 11623 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.348 AC: 52874 AN: 152136 Hom.: 11645 Cov.: 33 AF XY: 0.357 AC XY: 26566 AN XY: 74362

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.313

Alfa AF: 0.221 Hom.: 3068

Bravo AF: 0.359

Asia WGS AF: 0.579 AC: 2012 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	0.72
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: rs1107618; hg19: chr7-55280283;