rs2057999

Variant names:

• chr7-21334154-A-G
• rs2057999

Your query was ambiguous. Multiple possible variants found:

• chr7-21334154-A-G
• chr7-21334154-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 0.742 in 152,058 control chromosomes in the GnomAD database, including 43,215 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 0.74 (43215 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 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: 0.742 AC: 112806 AN: 151940 Hom.: 43188 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.742 AC: 112884 AN: 152058 Hom.: 43215 Cov.: 31 AF XY: 0.744 AC XY: 55271 AN XY: 74336

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.767

Alfa AF: 0.821 Hom.: 103917

Bravo AF: 0.731

Asia WGS AF: 0.703 AC: 2446 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057999; hg19: chr7-21373772;