rs1376544

chr4-178997397-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 0.489 in 151,828 control chromosomes in the GnomAD database, including 18,845 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 0.49 (18845 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 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: 0.489 AC: 74197 AN: 151710 Hom.: 18833 Cov.: 30

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.489 AC: 74238 AN: 151828 Hom.: 18845 Cov.: 30 AF XY: 0.490 AC XY: 36350 AN XY: 74202

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.480

Alfa AF: 0.508 Hom.: 3350

Bravo AF: 0.470

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376544; hg19: chr4-179918551;