rs7576189

Positions:

• chr2-217758165-C-T

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 0.938 in 152,174 control chromosomes in the GnomAD database, including 67,000 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 0.94 (67000 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142608 AN: 152056 Hom.: 66953 Cov.: 30

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.938 AC: 142713 AN: 152174 Hom.: 67000 Cov.: 30 AF XY: 0.941 AC XY: 69971 AN XY: 74384

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.941

Alfa AF: 0.944 Hom.: 10413

Bravo AF: 0.934

Asia WGS AF: 0.976 AC: 3394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.88
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7576189; hg19: chr2-218622888;