rs450378

Variant names:

• chr7-51941038-C-T
• rs450378

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 0.892 in 152,140 control chromosomes in the GnomAD database, including 61,585 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 0.89 (61585 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.892 AC: 135602 AN: 152022 Hom.: 61563 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.892 AC: 135671 AN: 152140 Hom.: 61585 Cov.: 31 AF XY: 0.894 AC XY: 66527 AN XY: 74376

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.951

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.888

Alfa AF: 0.940 Hom.: 20795

Bravo AF: 0.879

Asia WGS AF: 0.944 AC: 3283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs450378; hg19: chr7-52008734;