rs1990622

Positions:

• chr7-12244161-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;