rs450378

Variant names:

• chr7-51941038-C-T
• rs450378

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.697 AC: 28887 AN: 41446

American (AMR) AF: 0.925 AC: 14135 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3300 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5127 AN: 5164

South Asian (SAS) AF: 0.929 AC: 4471 AN: 4814

European-Finnish (FIN) AF: 0.996 AC: 10563 AN: 10608

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66228 AN: 68034

Other (OTH) AF: 0.888 AC: 1878 AN: 2114

Alfa AF: 0.935 Hom.: 25707

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs450378; hg19: chr7-52008734;