rs1551194

chr2-83677488-A-Gchr2-83677488-A-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 0.949 in 152,152 control chromosomes in the GnomAD database, including 68,737 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 0.95 (68737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 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: 0.949 AC: 144349 AN: 152034 Hom.: 68687 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.949 AC: 144455 AN: 152152 Hom.: 68737 Cov.: 32 AF XY: 0.947 AC XY: 70412 AN XY: 74364

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.954

Alfa AF: 0.963 Hom.: 8589

Bravo AF: 0.951

Asia WGS AF: 0.866 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.048
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551194; hg19: chr2-83904612;