rs2189915

Variant names:

• chr7-81372428-G-A
• rs2189915

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 0.253 in 151,650 control chromosomes in the GnomAD database, including 5,735 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 0.25 (5735 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.253 AC: 38348 AN: 151536 Hom.: 5739 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.253 AC: 38337 AN: 151650 Hom.: 5735 Cov.: 31 AF XY: 0.254 AC XY: 18790 AN XY: 74078

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.282

Alfa AF: 0.313 Hom.: 10530

Bravo AF: 0.236

Asia WGS AF: 0.166 AC: 577 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2189915; hg19: chr7-81001744;