rs1448822

chr4-110679942-A-Gchr4-110679942-A-T

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 0.622 in 151,932 control chromosomes in the GnomAD database, including 29,971 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 0.62 (29971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94454 AN: 151814 Hom.: 29957 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.622 AC: 94505 AN: 151932 Hom.: 29971 Cov.: 32 AF XY: 0.615 AC XY: 45694 AN XY: 74252

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.628

Alfa AF: 0.617 Hom.: 3861

Bravo AF: 0.629

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448822; hg19: chr4-111601098;