rs7577075

chr2-121820466-A-G

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 0.745 in 152,172 control chromosomes in the GnomAD database, including 43,499 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 0.75 (43499 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 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: 0.745 AC: 113288 AN: 152054 Hom.: 43456 Cov.: 34

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.745 AC: 113386 AN: 152172 Hom.: 43499 Cov.: 34 AF XY: 0.733 AC XY: 54529 AN XY: 74380

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.766

Alfa AF: 0.790 Hom.: 25279

Bravo AF: 0.739

Asia WGS AF: 0.515 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.36
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7577075; hg19: chr2-122578042;