rs7570682

Variant names:

• chr2-104366809-G-A
• rs7570682

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 0.308 in 151,938 control chromosomes in the GnomAD database, including 8,278 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 0.31 (8278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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 (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.307 AC: 46647 AN: 151820 Hom.: 8252 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.308 AC: 46729 AN: 151938 Hom.: 8278 Cov.: 32 AF XY: 0.305 AC XY: 22643 AN XY: 74288

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.290

Alfa AF: 0.231 Hom.: 9598

Bravo AF: 0.322

Asia WGS AF: 0.317 AC: 1102 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	0.56
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7570682; hg19: chr2-104983267;