rs7575840

chr2-21050618-G-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 0.258 in 152,108 control chromosomes in the GnomAD database, including 5,539 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 0.26 (5539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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: 0.258 AC: 39251 AN: 151990 Hom.: 5536 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.258 AC: 39266 AN: 152108 Hom.: 5539 Cov.: 32 AF XY: 0.255 AC XY: 18939 AN XY: 74364

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.229

Alfa AF: 0.304 Hom.: 7497

Bravo AF: 0.257

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.21
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7575840; hg19: chr2-21273490;