rs4976028

Positions:

• chr5-67994905-A-G
• chr5-67994905-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.185 in 152,158 control chromosomes in the GnomAD database, including 3,230 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 0.19 (3230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28222 AN: 152040 Hom.: 3233 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.185 AC: 28225 AN: 152158 Hom.: 3230 Cov.: 32 AF XY: 0.183 AC XY: 13640 AN XY: 74380

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0433

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.191

Alfa AF: 0.235 Hom.: 2435

Bravo AF: 0.180

Asia WGS AF: 0.110 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4976028; hg19: chr5-67290733;