rs7421966

Variant names:

• chr2-22745650-G-A
• rs7421966

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;