rs1220832

Variant names:

• chr4-69878239-A-T
• rs1220832

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 0.341 in 151,980 control chromosomes in the GnomAD database, including 8,933 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 0.34 (8933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 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: 0.341 AC: 51742 AN: 151860 Hom.: 8929 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.341 AC: 51775 AN: 151980 Hom.: 8933 Cov.: 33 AF XY: 0.340 AC XY: 25254 AN XY: 74278

African (AFR) AF: 0.360 AC: 14917 AN: 41466

American (AMR) AF: 0.397 AC: 6049 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1220 AN: 5152

South Asian (SAS) AF: 0.445 AC: 2146 AN: 4820

European-Finnish (FIN) AF: 0.286 AC: 3015 AN: 10556

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22237 AN: 67948

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.343 Hom.: 1174

Bravo AF: 0.347

Asia WGS AF: 0.329 AC: 1141 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.21
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1220832; hg19: chr4-70743957;