rs7421966

Positions:

• chr2-22745650-G-A

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 0.477 in 151,964 control chromosomes in the GnomAD database, including 18,156 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 0.48 (18156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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: 0.478 AC: 72528 AN: 151846 Hom.: 18150 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.477 AC: 72556 AN: 151964 Hom.: 18156 Cov.: 32 AF XY: 0.473 AC XY: 35128 AN XY: 74270

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.509

Alfa AF: 0.548 Hom.: 12399

Bravo AF: 0.470

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7421966; hg19: chr2-22968522;