rs400946

Variant names:

• chr22-21076765-T-C
• rs400946

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 0.798 in 152,282 control chromosomes in the GnomAD database, including 49,366 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 0.80 (49366 hom., cov: 34)
• Consequence: LOC112268300 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 11 publications found

Genes affected

LOC112268300 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641915.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284665	ENST00000641915.1		n.138+4116A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121474 AN: 152164 Hom.: 49320 Cov.: 34

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.798 AC: 121568 AN: 152282 Hom.: 49366 Cov.: 34 AF XY: 0.792 AC XY: 58982 AN XY: 74456

African (AFR) AF: 0.878 AC: 36474 AN: 41564

American (AMR) AF: 0.613 AC: 9383 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2425 AN: 5176

South Asian (SAS) AF: 0.739 AC: 3564 AN: 4822

European-Finnish (FIN) AF: 0.847 AC: 8974 AN: 10600

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55358 AN: 68028

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.801 Hom.: 219789

Bravo AF: 0.782

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.25
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs400946; hg19: chr22-21431054;