rs2322978

Variant names:

• chr11-127846245-A-G
• rs2322978

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.920 AC: 38199 AN: 41516

American (AMR) AF: 0.675 AC: 10317 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4364 AN: 5166

South Asian (SAS) AF: 0.865 AC: 4171 AN: 4820

European-Finnish (FIN) AF: 0.727 AC: 7690 AN: 10574

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.641 AC: 43586 AN: 67976

Other (OTH) AF: 0.734 AC: 1546 AN: 2106

Alfa AF: 0.676 Hom.: 50640

Bravo AF: 0.745

Asia WGS AF: 0.849 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2322978; hg19: chr11-127716140;