rs2057999

chr7-21334154-A-Gchr7-21334154-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;