chr4-59883111-A-T

Variant names:

• chr4-59883111-A-T
• rs10517480

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 0.272 in 151,924 control chromosomes in the GnomAD database, including 6,102 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 0.27 (6102 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.272 AC: 41314 AN: 151806 Hom.: 6093 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.272 AC: 41335 AN: 151924 Hom.: 6102 Cov.: 31 AF XY: 0.273 AC XY: 20270 AN XY: 74226

African (AFR) AF: 0.152 AC: 6304 AN: 41468

American (AMR) AF: 0.272 AC: 4144 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1772 AN: 5130

South Asian (SAS) AF: 0.379 AC: 1830 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3260 AN: 10538

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21748 AN: 67930

Other (OTH) AF: 0.307 AC: 648 AN: 2112

Alfa AF: 0.316 Hom.: 4178

Bravo AF: 0.263

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10517480; hg19: chr4-60748829;