rs1380148

Variant names:

• chr22-34446686-T-C
• rs1380148

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 0.417 in 151,592 control chromosomes in the GnomAD database, including 13,758 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 0.42 (13758 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.417 AC: 63173 AN: 151474 Hom.: 13731 Cov.: 30

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.417 AC: 63250 AN: 151592 Hom.: 13758 Cov.: 30 AF XY: 0.420 AC XY: 31131 AN XY: 74044

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.405

Alfa AF: 0.356 Hom.: 13661

Bravo AF: 0.430

Asia WGS AF: 0.393 AC: 1367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380148; hg19: chr22-34842677;