rs28373882

Variant names:

• chr4-67301618-T-C
• rs28373882

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0979 in 152,118 control chromosomes in the GnomAD database, including 939 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 0.098 (939 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.0980 AC: 14895 AN: 152000 Hom.: 939 Cov.: 30

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0979 AC: 14888 AN: 152118 Hom.: 939 Cov.: 30 AF XY: 0.0960 AC XY: 7142 AN XY: 74360

African (AFR) AF: 0.0271 AC: 1124 AN: 41518

American (AMR) AF: 0.0928 AC: 1417 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1535 AN: 10564

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.145 AC: 9887 AN: 67988

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.127 Hom.: 2120

Bravo AF: 0.0934

Asia WGS AF: 0.0180 AC: 66 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs28373882; hg19: chr4-68167336;