rs2207189

chr1-171419777-T-C

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 0.362 in 152,036 control chromosomes in the GnomAD database, including 10,681 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 0.36 (10681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.362 AC: 55048 AN: 151918 Hom.: 10674 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.362 AC: 55062 AN: 152036 Hom.: 10681 Cov.: 32 AF XY: 0.366 AC XY: 27220 AN XY: 74304

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.370

Alfa AF: 0.401 Hom.: 15450

Bravo AF: 0.354

Asia WGS AF: 0.349 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	11
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207189; hg19: chr1-171388916;