rs28373882

Positions:

• chr4-67301618-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0271

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.134 Hom.: 1574

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28373882; hg19: chr4-68167336;