rs2207189

Variant names:

• chr1-171419777-T-C
• rs2207189

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.227 AC: 9435 AN: 41522

American (AMR) AF: 0.424 AC: 6471 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1430 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4733 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27932 AN: 67952

Other (OTH) AF: 0.370 AC: 781 AN: 2112

Alfa AF: 0.393 Hom.: 39752

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2207189; hg19: chr1-171388916;