rs1448822

Variant names:

• chr4-110679942-A-G
• rs1448822

Your query was ambiguous. Multiple possible variants found:

• chr4-110679942-A-G
• chr4-110679942-A-T

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 0.622 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.513 AC: 21236 AN: 41422

American (AMR) AF: 0.683 AC: 10414 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2525 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2488 AN: 5148

South Asian (SAS) AF: 0.659 AC: 3173 AN: 4812

European-Finnish (FIN) AF: 0.568 AC: 5989 AN: 10546

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46452 AN: 67962

Other (OTH) AF: 0.628 AC: 1327 AN: 2114

Alfa AF: 0.613 Hom.: 3964

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1448822; hg19: chr4-111601098;