rs1376544

Variant names:

• chr4-178997397-C-T
• rs1376544

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;