rs2037719

Variant names:

• chr7-97089828-G-A
• rs2037719

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 0.239 in 152,058 control chromosomes in the GnomAD database, including 4,762 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 0.24 (4762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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: 0.239 AC: 36356 AN: 151936 Hom.: 4762 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.239 AC: 36362 AN: 152058 Hom.: 4762 Cov.: 32 AF XY: 0.240 AC XY: 17876 AN XY: 74336

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.248

Alfa AF: 0.274 Hom.: 8324

Bravo AF: 0.227

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037719; hg19: chr7-96719140;