rs1395479

chr4-177397037-C-Achr4-177397037-C-Gchr4-177397037-C-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 0.204 in 152,086 control chromosomes in the GnomAD database, including 3,927 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 0.20 (3927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 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: 0.204 AC: 31059 AN: 151968 Hom.: 3927 Cov.: 32

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.204 AC: 31058 AN: 152086 Hom.: 3927 Cov.: 32 AF XY: 0.206 AC XY: 15293 AN XY: 74334

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.231

Alfa AF: 0.256 Hom.: 8757

Bravo AF: 0.185

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.20
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395479; hg19: chr4-178318191;