rs2037719

Variant names:

• chr7-97089828-G-A
• rs2037719

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.150 AC: 6228 AN: 41494

American (AMR) AF: 0.235 AC: 3586 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3472

East Asian (EAS) AF: 0.109 AC: 566 AN: 5172

South Asian (SAS) AF: 0.277 AC: 1330 AN: 4808

European-Finnish (FIN) AF: 0.315 AC: 3324 AN: 10546

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19518 AN: 67980

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.266 Hom.: 18352

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2037719; hg19: chr7-96719140;