chr5-40908799-A-C

Variant names:

• chr5-40908799-A-C
• rs1376178

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 0.485 in 151,978 control chromosomes in the GnomAD database, including 19,106 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 0.48 (19106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73570 AN: 151860 Hom.: 19075 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.485 AC: 73661 AN: 151978 Hom.: 19106 Cov.: 32 AF XY: 0.482 AC XY: 35824 AN XY: 74292

African (AFR) AF: 0.693 AC: 28703 AN: 41430

American (AMR) AF: 0.449 AC: 6863 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1213 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2801 AN: 5174

South Asian (SAS) AF: 0.453 AC: 2189 AN: 4828

European-Finnish (FIN) AF: 0.372 AC: 3916 AN: 10540

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26469 AN: 67944

Other (OTH) AF: 0.460 AC: 972 AN: 2112

Alfa AF: 0.428 Hom.: 40897

Bravo AF: 0.502

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1376178; hg19: chr5-40908901;