rs2188245

chr7-104016039-C-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 0.0884 in 152,144 control chromosomes in the GnomAD database, including 1,328 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 0.088 (1328 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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: 0.0883 AC: 13428 AN: 152026 Hom.: 1323 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0884 AC: 13454 AN: 152144 Hom.: 1328 Cov.: 33 AF XY: 0.0941 AC XY: 7001 AN XY: 74390

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0496 Hom.: 65

Bravo AF: 0.105

Asia WGS AF: 0.210 AC: 729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.82
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188245; hg19: chr7-103656486;