rs1990622

Variant names:

• chr7-12244161-A-G
• rs1990622

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 0.517 in 152,024 control chromosomes in the GnomAD database, including 21,670 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 0.52 (21670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.517 AC: 78477 AN: 151906 Hom.: 21639 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.517 AC: 78566 AN: 152024 Hom.: 21670 Cov.: 32 AF XY: 0.518 AC XY: 38510 AN XY: 74312

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.489

Alfa AF: 0.451 Hom.: 7608

Bravo AF: 0.540

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1990622; hg19: chr7-12283787;