rs2322978

Variant names:

• chr11-127846245-A-G
• rs2322978

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 0.745 in 152,114 control chromosomes in the GnomAD database, including 43,423 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 0.74 (43423 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 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: 0.745 AC: 113196 AN: 151996 Hom.: 43357 Cov.: 31

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.745 AC: 113321 AN: 152114 Hom.: 43423 Cov.: 31 AF XY: 0.749 AC XY: 55740 AN XY: 74378

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.734

Alfa AF: 0.659 Hom.: 32287

Bravo AF: 0.745

Asia WGS AF: 0.849 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2322978; hg19: chr11-127716140;