rs7577075

Variant names:

• chr2-121820466-A-G
• rs7577075

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;