5-42400204-T-C

Variant names:

• chr5-42400204-T-C
• rs2972395

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;