5-42071409-T-C

Variant names:

• chr5-42071409-T-C
• rs275025

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 0.804 in 151,862 control chromosomes in the GnomAD database, including 49,260 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 0.80 (49260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122054 AN: 151744 Hom.: 49214 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.804 AC: 122159 AN: 151862 Hom.: 49260 Cov.: 31 AF XY: 0.806 AC XY: 59812 AN XY: 74228

African (AFR) AF: 0.801 AC: 33197 AN: 41426

American (AMR) AF: 0.813 AC: 12376 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2690 AN: 3458

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5180

South Asian (SAS) AF: 0.862 AC: 4158 AN: 4826

European-Finnish (FIN) AF: 0.812 AC: 8594 AN: 10578

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53471 AN: 67852

Other (OTH) AF: 0.784 AC: 1655 AN: 2110

Alfa AF: 0.790 Hom.: 5906

Bravo AF: 0.805

Asia WGS AF: 0.928 AC: 3225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs275025; hg19: chr5-42071511;