5-42400204-T-C

Position:

• chr5-42400204-T-C

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 0.823 in 152,110 control chromosomes in the GnomAD database, including 51,726 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 0.82 (51726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.823 AC: 125036 AN: 151992 Hom.: 51672 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.823 AC: 125148 AN: 152110 Hom.: 51726 Cov.: 31 AF XY: 0.830 AC XY: 61685 AN XY: 74362

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.807

Alfa AF: 0.820 Hom.: 6382

Bravo AF: 0.814

Asia WGS AF: 0.930 AC: 3232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2972395; hg19: chr5-42400306;