rs4976028

Variant names:

• chr5-67994905-A-G
• rs4976028

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;