rs7575840

Variant names:

• chr2-21050618-G-T
• rs7575840

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;