rs7285004

Variant names:

• chr22-44378820-T-C
• rs7285004

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 0.396 in 152,038 control chromosomes in the GnomAD database, including 12,572 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 0.40 (12572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 0.396 AC: 60092 AN: 151920 Hom.: 12561 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.396 AC: 60137 AN: 152038 Hom.: 12572 Cov.: 32 AF XY: 0.402 AC XY: 29868 AN XY: 74320

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.403

Alfa AF: 0.390 Hom.: 20724

Bravo AF: 0.407

Asia WGS AF: 0.555 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7285004; hg19: chr22-44774700;