rs1107617

chr7-55212575-A-Cchr7-55212575-A-G

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 0.135 in 152,270 control chromosomes in the GnomAD database, including 1,918 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 0.13 (1918 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.135 AC: 20487 AN: 152152 Hom.: 1913 Cov.: 34

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20521 AN: 152270 Hom.: 1918 Cov.: 34 AF XY: 0.138 AC XY: 10278 AN XY: 74454

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.134

Alfa AF: 0.103 Hom.: 1172

Bravo AF: 0.142

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.3
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107617; hg19: chr7-55280268;