rs1375749

Positions:

• chr4-176540214-A-G

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 0.241 in 151,280 control chromosomes in the GnomAD database, including 5,300 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 0.24 (5300 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 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: 0.241 AC: 36383 AN: 151160 Hom.: 5294 Cov.: 29

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.241 AC: 36397 AN: 151280 Hom.: 5300 Cov.: 29 AF XY: 0.239 AC XY: 17636 AN XY: 73916

Gnomad4 AFR AF: 0.0954

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.240

Alfa AF: 0.302 Hom.: 6972

Bravo AF: 0.231

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1375749; hg19: chr4-177461365;