rs2188245

Variant names:

• chr7-104016039-C-G
• rs2188245

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;